The Protein Databank

1
The Protein Databank

• Working with protein data-files

2
Determining Biomolecule Structures

• X-ray crystallography
• Nuclear magnetic resonance

3
The Protein Databank
4
The PDB Growth Chart

• figGROWTH.eps

5
Maxim 10.1

• Beware of anything in the PDB Header Section

6
The PDB Data-File Formats
7
Example PDB structure 1LQT

• fig1LQT.eps

8
Example PDB structure 1M7T

• fig1M7T.eps

9
Downloading PDB data-files

• http//www.rcsb.org/pdb/
• http//www.ebi.ac.uk/services/

10
Accessing Data In PDB Entries

• Accessing PDB Annotation Data
• Free R and resolution

11
Example PDB data-file

• REMARK 2
• REMARK 2 RESOLUTION. 1.05 ANGSTROMS.
• REMARK 215 NMR STUDY
• REMARK 215 THE COORDINATES IN THIS ENTRY WERE
  GENERATED FROM SOLUTION
• REMARK 215 NMR DATA. PROTEIN DATA BANK
  CONVENTIONS REQUIRE THAT
• REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED,
  BUT THE VALUES ON
• REMARK 215 THESE RECORDS ARE MEANINGLESS.

12
Example PDB data-file, cont.

• .
• .
• .
• REMARK 3 FIT TO DATA USED IN REFINEMENT.
• REMARK 3 CROSS-VALIDATION METHOD THROUGHOUT
• REMARK 3 FREE R VALUE TEST SET SELECTION RANDOM
  
• REMARK 3 R VALUE (WORKING TEST SET) 0.134
• REMARK 3 R VALUE (WORKING SET) 0.134
• REMARK 3 FREE R VALUE 0.153
• REMARK 3 FREE R VALUE TEST SET SIZE () NULL
• REMARK 3 FREE R VALUE TEST SET COUNT 2200
• .
• .
• .

13
Plotting Free R Values against Resolution

• figFREER.eps

14
Database cross references

• DBREF 1LQT A 1 456 GB 13882996 AAK47528 1 456
• DBREF 1LQT B 1 456 GB 13882996 AAK47528 1 456
• DBREF 1AFI 1 72 SWS P04129 MERP_SHIFL 20 91
• DBREF 1M7T A 1 66 SWS P10599 THIO_HUMAN 0 65
• DBREF 1M7T A 67 106 SWS P00274 THIO_ECOLI 68 107

15
Coordinates section

• REMARK 210
• REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS
  ENSEMBLE 21
• REMARK 210

16
Data section

• ATOM 1 N ARG A 2 26.318 -8.010 39.090 1.00 20.71
  N
• ANISOU 1 N ARG A 2 2040 3071 2755 114 -339 -393 N
  
• ATOM 2 CA ARG A 2 25.150 -8.702 38.505 1.00 18.85
  C
• ANISOU 2 CA ARG A 2 2029 2677 2455 67 -321 -209 C
  
• ATOM 3 C ARG A 2 24.846 -8.176 37.123 1.00 17.23
  C
• ANISOU 3 C ARG A 2 1689 2429 2429 143 -282 -258 C
  
• ATOM 4 O ARG A 2 25.151 -7.048 36.775 1.00 18.14
  O
• .
• .
• TER 7215 GLY A 456
• ATOM 7216 N ARG B 2 -19.423 25.709 6.980 1.00
  21.57 N
• ANISOU 7216 N ARG B 2 2476 3012 2707 -165 -370 95
  N
• ATOM 7217 CA ARG B 2 -18.718 26.510 8.024 1.00
  19.01 C
• ANISOU 7217 CA ARG B 2 2127 2672 2424 -63 -285 91
  C
• ATOM 7218 C ARG B 2 -17.250 26.207 8.002 1.00
  17.22 C
• ANISOU 7218 C ARG B 2 1955 2392 2196 -91 -299 121
  C
• ATOM 7219 O ARG B 2 -16.851 25.158 7.535 1.00
  18.15 O

17
Data section, cont.

• TER 14289 GLY B 456
• HETATM14290 C ACT 1866 -13.075 1.733 10.218 1.00
  27.25 C
• ANISOU14290 C ACT 1866 3493 3560 3299 -39 -36 -44
  C
• .
• .
• CONECT14290142911429214293
• CONECT1429114290
• CONECT1429214290
• TER
• .
• .
• CONECT1469014663
• MASTER 389 0 15 46 38 0 0 620280 2 401 72
• END

18
Data section, cont.

• MODEL 1
• ATOM 1 N MET A 1 3.110 -4.682 -3.025 1.00 0.00 N
• ATOM 2 CA MET A 1 2.546 -3.712 -2.053 1.00 0.00 C
  
• ATOM 3 C MET A 1 1.134 -3.295 -2.450 1.00 0.00 C
• ATOM 4 O MET A 1 0.882 -2.130 -2.758 1.00 0.00 O
• ATOM 5 CB MET A 1 3.466 -2.491 -2.002 1.00 0.00 C
  
• ATOM 6 CG MET A 1 3.781 -1.903 -3.370 1.00 0.00 C
  
• ATOM 7 SD MET A 1 4.256 -0.166 -3.285 1.00 0.00 S
  
• ATOM 8 CE MET A 1 6.004 -0.307 -2.920 1.00 0.00 C
  
• ATOM 9 1H MET A 1 2.906 -4.327 -3.980 1.00 0.00 H
  
• ATOM 10 2H MET A 1 2.650 -5.601 -2.859 1.00 0.00
  H
• ATOM 11 3H MET A 1 4.134 -4.738 -2.858 1.00 0.00
  H
• ATOM 12 HA MET A 1 2.517 -4.178 -1.079 1.00 0.00
  H
• ATOM 13 1HB MET A 1 2.996 -1.724 -1.405 1.00 0.00
  H
• ATOM 14 2HB MET A 1 4.397 -2.778 -1.536 1.00 0.00
  H
• ATOM 15 1HG MET A 1 4.596 -2.461 -3.807 1.00 0.00
  H
• ATOM 16 2HG MET A 1 2.907 -1.993 -3.998 1.00 0.00
  H
• ATOM 17 1HE MET A 1 6.344 -1.302 -3.167 1.00 0.00
  H
• ATOM 18 2HE MET A 1 6.169 -0.120 -1.869 1.00 0.00
  H

19
Data section, cont.

• TER 1659 VAL A 107
• ENDMDL
• MODEL 2
• ATOM 1 N MET A 1 2.750 -6.779 -1.627 1.00 0.00 N
• ATOM 2 CA MET A 1 2.487 -5.475 -2.290 1.00 0.00 C
  
• .
• .
• .
• TER 1660 VAL A 107
• ENDMDL

20
Extracting 3D co-ordinate data

• my ( X, Y, Z ) ( substr( _, 30, 8 ),
• substr( _, 38, 8 ),
• substr( _, 46, 8 ) )

21
The simple_coord_extract program

• ! /usr/bin/perl -w
• simple_coord_extract ltPDB Filegt - Demonstrates
  the extraction of
• C-Alpha co-ordinates from a PDB
• data-file.
• use strict
• while ( ltgt )
• if ( /ATOM/ substr( _, 13, 4 ) eq "CA "
  )
• my ( X, Y, Z ) ( substr( _, 30, 8
  ),
• substr( _, 38, 8 ),
• substr( _, 46, 8 ) )
• X s/ //g
• Y s/ //g
• Z s/ //g

22
Results from simple_coord_extract ...

• X, Y Z 25.150, -8.702, 38.505
• X, Y Z 23.675, -8.497, 35.069
• X, Y Z 20.747, -6.252, 34.332
• X, Y Z 17.545, -8.297, 34.292
• X, Y Z 15.182, -7.484, 31.454
• X, Y Z 11.736, -8.952, 30.942
• X, Y Z 10.261, -9.014, 27.451
• X, Y Z 6.507, -9.548, 27.173

23
The graphic image contact map

• figCONTACTMAP.eps

24
STRIDE Secondary Structure Assignment
25
Maxim 10.2

• It is often easier and desirable to regenerate
  database annotation than trawl through entries
  reconstituting the annotation using custom code.

26
Installation of STRIDE

• tar -zxvf stride.tar.gz
• cd stride
• make
• ./stride

27
Assigning Secondary Structures
28
Simplified definition of a Hydrogen Bond

• figSIMPLIFIED.eps

29
Example of Secondary Structure Elements in
Proteins

• figSSDEMO.eps

30
Definition of Dihedral angles in the backbone of
protein structures

• figPSIPSI.eps

31
Using STRIDE and parsing the output

• ./stride
• You must specify input file
• Action secondary structure assignment
• Usage stride Options InputFile gt file
• Options
• -f File Output file
• -mFile MolScript file
• -o Report secondary structure summary
  Only
• -h Report Hydrogen bonds
• -rId1Id2.. Read only chains Id1, Id2 ...
• -cId1Id2.. Process only Chains Id1, Id2 ...
• -qFile Generate SeQuence file in FASTA
  format and die
• Options are position and case insensitive
• stride -cA 1lqt.pdb

32
Using gawk ...

• gawk '/ASG/ print 8 " " 9' 1lqt.A.stride
• 360.00 156.52
• -75.72 161.36
• -71.26 145.24
• -111.08 119.10
• -118.65 131.78
• .
• .
• gawk '(/ASG/ /Strand/) print 8 " " 9'
  1lqt.A.stride
• gawk '(/ASG/ /AlphaHelix/) print 8 " "
  9' 1lqt.A.stride

33
Ramachandran Plot of dihedral angles of chain A
from 1LQT

• fig1LQTPHIPSI.eps

34
Extracting amino acid sequences using STRIDE

• stride -q 1lqt.pdb
• gt1lqt.pdb A 452 1.050
• RPYYIAIVGSGPSAFFAAASLLKAADTTEDLDMAVDMLEMLPTPWGLVRS
  GVAPDHPKIK
• .
• .
• gt1lqt.pdb B 454 1.050
• RPYYIAIVGSGPSAFFAAASLLKAADTTEDLDMAVDMLEMLPTPWGLVRS
  GVAPDHPKIK
• .
• .
• stride -cA -q 1lqt.pdb
• gt1lqt.pdb A 452 1.050
• RPYYIAIVGSGPSAFFAAASLLKAADTTEDLDMAVDMLEMLPTPWGLVRS
  GVAPDHPKIK
• .
• .

35
Introducing The mmCIF Protein Format
36
Converting mmCIF

• Converting mmCIF to PDB
• Converting mmCIFs to PDB with CIFTr

37
The CIFTr program

• cd
• tar -zxvf ciftr-v2.0-linux.tar.gz
• cd ciftr-v2.0-linux/
• setenv RCSBROOT /ciftr-v2.0-linux
• export RCSBROOT /ciftr-v2.0-linux
• ./CIFTr -i 1lqt.cif

38
More on mmCIF

• Problems with the CIFTr conversion
• Some advice on using mmCIF
• Automated conversion of mmCIF to PDB

39
Where To From Here