PDB Atomic Coordinate Entry Format Guide v3.30

Protein Data Bank Contents Guide:
Atomic Coordinate Entry Format Description
Version 3.30
Document Published by the wwPDB
This format complies with the PDB Exchange Dictionary (PDBx)
http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Index/index.html.
©2008 wwPDB

PDB File Format v. 3.3
Page i
Table of Contents
1. Introduction ................................................................................................................................... 1!
Basic Notions of the Format Description ............................................................................................ 3!
Record Format .................................................................................................................................... 5!
Types of Records ............................................................................................................................... 6!
PDB Format Change Policy ................................................................................................................ 9!
Order of Records .............................................................................................................................. 10!
Sections of an Entry ......................................................................................................................... 12!
Field Formats and Data Types ......................................................................................................... 14!
2. Title Section ................................................................................................................................ 16!
HEADER ........................................................................................................................................... 16!
OBSLTE ........................................................................................................................................... 19!
TITLE ................................................................................................................................................ 21!
SPLIT (added) .................................................................................................................................. 22!
CAVEAT ........................................................................................................................................... 23!
COMPND (updated) ......................................................................................................................... 24!
SOURCE (updated) .......................................................................................................................... 26!
KEYWDS .......................................................................................................................................... 31!
EXPDTA (updated) ........................................................................................................................... 33!
NUMMDL (added) ............................................................................................................................ 35!
MDLTYP (added) .............................................................................................................................. 36!
AUTHOR .......................................................................................................................................... 38!
REVDAT (updated) ........................................................................................................................... 40!
SPRSDE ........................................................................................................................................... 42!
JRNL (updated) ................................................................................................................................ 44!
REMARK .......................................................................................................................................... 52!
REMARKs 0-5 ......................................................................................................................... 52!
REMARK 0 (added), Re-refinement notice ............................................................................... 52!
REMARK 1 (updated), Related publications ............................................................................. 54!
REMARK 2 (updated), Resolution ............................................................................................ 60!
REMARK 3 (updated), Final refinement information ................................................................. 61!
Refinement using X-PLOR ........................................................................................................ 62!
Refinement using CNS .............................................................................................................. 64!
Refinement using CNX .............................................................................................................. 66!
Refinement using REFMAC ...................................................................................................... 68!
Refinement using NUCLSQ ...................................................................................................... 76!
Refinement using SHELXL ....................................................................................................... 80!
Refinement using TNT/BUSTER ............................................................................................... 82!
Refinement using PHENIX ........................................................................................................ 85!
Refinement using BUSTER-TNT .............................................................................................. 93!
Example for Solution Scattering ................................................................................................ 98!
Non-diffraction studies .............................................................................................................. 98!
REMARK 4 (updated), Format .................................................................................................. 99!
REMARK 5 (updated), Obsolete Statement .............................................................................. 99!

PDB File Format v. 3.3
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REMARKs 6 - 99 ................................................................................................................... 100!
REMARK 100 (updated), Deposition or Processing Site ...................................................... 100!
REMARKs 200-265, Experimental Details ............................................................................ 101!
REMARK 200 (updated), X-ray Diffraction Experimental Details ............................................ 101!
REMARK 205, Fiber Diffraction, Fiber Sample Experiment Details ........................................ 104!
REMARKs 210 and 215/217, NMR Experiment Details .......................................................... 104!
REMARK 230, Neutron Diffraction Experiment Details ........................................................... 106!
REMARK 240 (updated), Electron Crystallography Experiment Details ................................. 109!
REMARK 245 (updated), Electron Microscopy Experiment Details ........................................ 111!
REMARK 247, Electron Microscopy details ............................................................................ 113!
REMARK 250, Other Type of Experiment Details ................................................................... 113!
REMARK 265, Solution Scattering Experiment Details .......................................................... 114!
REMARKs 280-290, Crystallographic Details ....................................................................... 116!
REMARK 280, Crystal ............................................................................................................. 116!
REMARK 285, CRYST1 .......................................................................................................... 116!
REMARK 290, Crystallographic Symmetry ............................................................................. 117!
REMARK 300 (updated), Biomolecule .................................................................................... 118!
REMARK 350 (updated), Generating the Biomolecule ........................................................... 120!
Example – When software predicts multiple quaternary assemblies ...................................... 122!
REMARK 375 (updated), Special Position .............................................................................. 124!
REMARK 400, Compound ...................................................................................................... 124!
REMARK 450, Source ............................................................................................................ 126!
REMARK 465 (updated), Missing residues ............................................................................. 126!
REMARK 470 (updated), Missing Atom(s) .............................................................................. 127!
REMARK 475 (added), Residues modeled with zero occupancy ........................................... 128!
REMARK 480 (added), Polymer atoms modeled with zero occupancy .................................. 129!
REMARK 500 (updated), Geometry and Stereochemistry ...................................................... 130!
REMARK 525 (updated), Distant Solvent Atoms .................................................................... 136!
REMARK 600, Heterogen ....................................................................................................... 136!
REMARK 610, Non-polymer residues with missing atoms ..................................................... 138!
REMARK 615, Non-polymer residues containing atoms with zero occupancy ....................... 138!
REMARK 620 (added), Metal coordination ............................................................................. 139!
REMARK 630 (added), Inhibitor Description ........................................................................... 141!
REMARK 650, Helix ................................................................................................................ 142!
REMARK 700, Sheet .............................................................................................................. 143!
REMARK 800 (updated), Important Sites ............................................................................... 145!
REMARK 999, Sequence ........................................................................................................ 147!
3. Primary Structure Section ......................................................................................................... 148!
DBREF (standard format) ............................................................................................................... 148!
DBREF1 / DBREF2 (added) ........................................................................................................... 151!
SEQADV ......................................................................................................................................... 152!
SEQRES (updated) ........................................................................................................................ 155!
MODRES (updated) ....................................................................................................................... 157!
4. Heterogen Section (updated) .................................................................................................... 159!
HET ................................................................................................................................................ 159!
HETNAM ........................................................................................................................................ 161!

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HETSYN ......................................................................................................................................... 163!
FORMUL ........................................................................................................................................ 164!
5. Secondary Structure Section ..................................................................................................... 166!
HELIX ............................................................................................................................................. 166!
SHEET ............................................................................................................................................ 168!
6. Connectivity Annotation Section ............................................................................................... 171!
SSBOND (updated) ........................................................................................................................ 171!
LINK (updated) ............................................................................................................................... 173!
CISPEP .......................................................................................................................................... 175!
7. Miscellaneous Features Section ............................................................................................... 177!
SITE ................................................................................................................................................ 177!
8. Crystallographic and Coordinate Transformation Section ......................................................... 179!
CRYST1 ......................................................................................................................................... 179!
ORIGXn .......................................................................................................................................... 181!
SCALEn .......................................................................................................................................... 182!
MTRIXn .......................................................................................................................................... 184!
9. Coordinate Section .................................................................................................................... 185!
MODEL ........................................................................................................................................... 185!
ATOM ............................................................................................................................................. 187!
ANISOU .......................................................................................................................................... 190!
TER ................................................................................................................................................ 192!
HETATM ......................................................................................................................................... 194!
ENDMDL ........................................................................................................................................ 196!
10. Connectivity Section ................................................................................................................ 197!
CONECT ........................................................................................................................................ 197!
11. Bookkeeping Section .............................................................................................................. 199!
MASTER ......................................................................................................................................... 199!
END ................................................................................................................................................ 201!

PDB File Format v. 3.3
Page 1
1. Introduction
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional
structures of biological macromolecules that serves a global community of researchers, educators,
and students. The data contained in the archive include atomic coordinates, crystallographic structure
factors and NMR experimental data. Aside from coordinates, each deposition also includes the
names of molecules, primary and secondary structure information, sequence database references,
where appropriate, and ligand and biological assembly information, details about data collection and
structure solution, and bibliographic citations.
This comprehensive guide describes the "PDB format" used by the members of the worldwide Protein
Data Bank (wwPDB; Berman, H.M., Henrick, K. and Nakamura, H. Announcing the worldwide Protein
Data Bank. Nat Struct Biol 10, 980 (2003)). Questions should be sent to [email protected]
Information about file formats and data dictionaries can be found at http://wwpdb.org.
Version History:
Version 2.3: The format in which structures were released from 1998 to July 2007.
Version 3.0: Major update from Version 2.3; incorporates all of the revisions used by the wwPDB to
integrate uniformity and remediation data into a single set of archival data files including IUPAC
nomenclature. See http://www.wwpdb.org/docs.html for more details.
Version 3.1: Minor addenda to Version 3.0, introducing a small number of changes and extensions
supporting the annotation practices adopted by the wwPDB beginning in August 2007 including chain
ID standardization and biological assembly .
Version 3.15: Minor addenda to Version 3.20, introducing a small number of changes and extensions
supporting the annotation practices adopted by the wwPDB beginning in October 2008 including
DBREF, taxonomy and citation information.
Version 3.20: Minor addenda to Version 3.1, introducing a small number of changes and extensions
supporting the annotation practices adopted by the wwPDB beginning in December 2008 including
DBREF, taxonomy and citation information.
September 15 2008, initial version 3.20.
November 15 2008, add examples for Refmac template and coordinate with alternate
conformation.
December 24 2008, update REMARK 3 templates/examples, add Norine database in DBREF,
update REMARK 500 on chiral center.
February 12 2009, update example in REMARK 210 and record format in NUMMDL
July 6 2009, update description for REVDAT, DBREF2, MASTER and extend number of
columns for AUTHOR, JRNL, CAVEAT, KEYWDS, etc.
December 22, 2009, update CAVEAT and REMARK 265.
April 21, 2010, update REMARK 5 and add BUSTER-TNT template in REMARK 3.