1O64

Crystal structure of an ATP phosphoribosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural analysis of a set of proteins resulting from a bacterial genomics project

Badger, J.Sauder, J.M.Adams, J.M.Antonysamy, S.Bain, K.Bergseid, M.G.Buchanan, S.G.Buchanan, M.D.Batiyenko, Y.Christopher, J.A.Emtage, S.Eroshkina, A.Feil, I.Furlong, E.B.Gajiwala, K.S.Gao, X.He, D.Hendle, J.Huber, A.Hoda, K.Kearins, P.Kissinger, C.Laubert, B.Lewis, H.A.Lin, J.Loomis, K.Lorimer, D.Louie, G.Maletic, M.Marsh, C.D.Miller, I.Molinari, J.Muller-Dieckmann, H.J.Newman, J.M.Noland, B.W.Pagarigan, B.Park, F.Peat, T.S.Post, K.W.Radojicic, S.Ramos, A.Romero, R.Rutter, M.E.Sanderson, W.E.Schwinn, K.D.Tresser, J.Winhoven, J.Wright, T.A.Wu, L.Xu, J.Harris, T.J.

(2005) Proteins 60: 787-796

  • DOI: 10.1002/prot.20541
  • Primary Citation of Related Structures:  1O60, 1O61, 1O62, 1O63, 1O65, 1O66, 1O67, 1O68, 1O69, 1O6B, 1O6C, 1O6D, 1VGT, 1VGU, 1VGV, 1VGW, 1VGX, 1VGY, 1VGZ, 1VH0, 1VH1, 1VH2, 1VH3, 1VH4, 1VH5, 1VH6, 1VH7, 1VH8, 1VH9, 1VHA, 1VHC, 1VHD, 1VHE, 1VHF, 1VHG, 1VHJ, 1VHK, 1VHL, 1VHM, 1VHO, 1VHQ, 1VHS, 1VHT, 1VHU, 1VHV, 1VHW, 1VHX, 1VHY, 1VHZ, 1VI0, 1VI1, 1VI2, 1VI3, 1VI4, 1VI5, 1VI6, 1VI8, 1VI9, 1VIA, 1VIC, 1VIM, 1VIQ, 1VIS, 1VIU, 1VIV, 1VIX, 1VIY, 1VIZ
  • Also Cited By: 1INN, 1J6V, 1J6W, 1J6X, 1MDO, 1MDX, 1MDZ, 1VHN, 1VI7, 1VIO, 1VJE

  • PubMed Abstract: 
  • The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures ...

    The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.


    Organizational Affiliation

    Structural GenomiX Inc., San Diego, California, USA. jbadger@active-sight.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP phosphoribosyltransferase
A, B
219Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: hisG
EC: 2.4.2.17
Find proteins for Q9X0D2 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X0D2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.183α = 90.00
b = 50.398β = 94.60
c = 76.794γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
TRUNCATEdata scaling
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-10-23 
  • Released Date: 2003-11-11 
  • Deposition Author(s): Structural GenomiX

Revision History 

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description