3AW8

Crystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb3AW8/pdb

• Classification: LIGASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-15 Released: 2012-04-11 
• Deposition Author(s): Okada, K., Tsunoda, S., Taka, H., Baba, S., Kanagawa, M., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.255 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Crystal structures of N5-carboxyaminoimidazole ribonucleotide synthetase, PurK, from thermophilic bacteria

Okada, K., Taka, H., Tsunoda, S., Tamura, S., Miyazawa, R., Baba, S., Kanagawa, M., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 81.1 kDa 
• Atom Count: 5,804 
• Modelled Residue Count: 720 
• Deposited Residue Count: 738 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase, ATPase subunit	A, B	369	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0513 EC: 6.3.4.18
UniProt
Find proteins for Q5SKY0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKY0  Go to UniProtKB:  Q5SKY0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], E [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
CL	D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.255 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.26	α = 90
b = 81.26	β = 90
c = 203.163	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Okada, K., Tsunoda, S., Taka, H., Baba, S., Kanagawa, M., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Derived calculations