5AVM

Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, PurM, from Thermus thermophilus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 

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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.

(2016) J Biochem 159: 313-321

  • DOI: 10.1093/jb/mvv107
  • Primary Citation of Related Structures:  
    2Z01, 5AVM

  • 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 with four dimers in an asymmetric unit ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoribosylformylglycinamidine cyclo-ligase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
333Thermus thermophilus HB8Mutation(s): 0 
Gene Names: purM, TTHA0367
EC: 6.3.3.1
UniProt
Find proteins for Q5SLC6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLC6 
Go to UniProtKB:  Q5SLC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLC6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.328α = 90
b = 142.63β = 90
c = 218.616γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data processing
HKL-2000data scaling
AMoREphasing
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Derived calculations