2Z01

Crystal structure of phosphoribosylaminoimidazole synthetase from Geobacillus kaustophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus

Kanagawa, M.Baba, S.Watanabe, Y.Nakagawa, N.Ebihara, A.Kuramitsu, S.Yokoyama, S.Sampei, G.Kawai, G.

(2015) J.Biochem. --: --

  • DOI: 10.1093/jb/mvv107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, also known as PurM, from Thermus thermophilus (Tt) and Geobacillus kaustophilus (Gk) were determined. For TtPurM, the maximum resolution was 2.2 Å and the space group was P21212 ...

    Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, also known as PurM, from Thermus thermophilus (Tt) and Geobacillus kaustophilus (Gk) were determined. For TtPurM, the maximum resolution was 2.2 Å and the space group was P21212 with four dimers in an asymmetric unit. For GkPurM, the maximum resolution was 2.2 Å and the space group was P21212 with one monomer in asymmetric unit. The biological unit is dimer for both TtPurM and GkPurM and the dimer structures were similar to previously determined structures of PurM in general. For TtPurM, ∼50 residues at the amino terminal were disordered in the crystal structure whereas, for GkPurM, the corresponding region covered the ATP-binding site forming an α helix in part, suggesting that the N-terminal region of PurM changes its conformation upon binding of ligands. FGAM binding site was predicted by the docking simulation followed by the MD simulation based on the SO4 (2-) binding site found in the crystal structure of TtPurM.


    Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan; gkawai@sea.it-chiba.ac.jp.,Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; and.,RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan sampei@pc.uec.ac.jp.,RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan;,Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan;,RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan; and.,RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5148, Japan; Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Sayo, Hyogo 679-5198, Japan;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoribosylformylglycinamidine cyclo-ligase
A
348Geobacillus kaustophilus (strain HTA426)Mutation(s): 0 
Gene Names: purM
EC: 6.3.3.1
Find proteins for Q5L3D0 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5L3D0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.106α = 90.00
b = 111.107β = 90.00
c = 53.326γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-11-25
    Type: Database references