3AX6 | pdb_00003ax6

Crystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb3AX6/pdb

• Classification: LIGASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-30 Released: 2012-04-25 
• Deposition Author(s): Miyazawa, R., Kanagawa, M., Baba, S., 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: 2.20 Å
• R-Value Free: 
  0.268 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 174.23 kDa 
• Atom Count: 12,259 
• Modeled Residue Count: 1,438 
• Deposited Residue Count: 1,520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase, ATPase subunit	A, B, C, D	380	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM_0447 EC: 6.3.4.18
UniProt
Find proteins for Q9WYS8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYS8  Go to UniProtKB:  Q9WYS8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], F [auth B], G [auth C], H [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.268 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.919	α = 90
b = 186.59	β = 90.49
c = 68.463	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Miyazawa, R., Kanagawa, M., Baba, S., Nakagawa, N., Ebihara, A., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary