2Z02 | pdb_00002z02

Crystal structure of phosphoribosylaminoimidazolesuccinocarboxamide synthase wit ATP from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb2Z02/pdb

• Classification: LIGASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-06 Released: 2007-11-06 
• Deposition Author(s): Kanagawa, M., Baba, S., 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: 2.03 Å
• R-Value Free: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of phosphoribosylaminoimidazolesuccinocarboxamide synthase from Methanocaldococcus jannaschii

Kanagawa, M., Baba, S., 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: 57.1 kDa 
• Atom Count: 4,301 
• Modeled Residue Count: 484 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole-succinocarboxamide synthase	A, B	242	Methanocaldococcus jannaschii	Mutation(s): 0  EC: 6.3.2.6
UniProt
Find proteins for Q58987 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58987  Go to UniProtKB:  Q58987

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A], G [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CIT	H [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.099	α = 90
b = 82.099	β = 90
c = 85.152	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): Kanagawa, M., Baba, S., Kuramitsu, S., Yokoyama, S., Kawai, G., Sampei, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description