2DPL | pdb_00002dpl

Crystal Structure of the GMP synthase from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb2DPL/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-12 Released: 2006-11-12 
• Deposition Author(s): Asada, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the GMP synthase from Pyrococcus horikoshii OT3

Asada, Y., Kunishima, N.

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: 69.22 kDa 
• Atom Count: 5,452 
• Modeled Residue Count: 565 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP synthase [glutamine-hydrolyzing] subunit B	A, B	308	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: guaAB EC: 6.3.5.2
UniProt
Find proteins for O59072 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59072  Go to UniProtKB:  O59072

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.4	α = 90
b = 83.334	β = 90
c = 112.255	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-12 
Deposition Author(s): Asada, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-11-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description