2CXX | pdb_00002cxx

Crystal structure of a probable GTP-binding protein engB

• PDB DOI: https://doi.org/10.2210/pdb2CXX/pdb

• Classification: CELL CYCLE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-07-01 Released: 2006-01-01 
• Deposition Author(s): Kukimoto-Niino, M., Murayama, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of a probable GTP-binding protein engB

Kukimoto-Niino, M., Murayama, K., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.08 kDa 
• Atom Count: 5,054 
• Modeled Residue Count: 539 
• Deposited Residue Count: 570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable GTP-binding protein engB	A, B, C	190	Pyrococcus horikoshii OT3	Mutation(s): 4
UniProt
Find proteins for O57939 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57939  Go to UniProtKB:  O57939

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], E [auth B], F [auth C]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.357	α = 90
b = 75.357	β = 90
c = 79.112	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-01 
Deposition Author(s): Kukimoto-Niino, M., Murayama, K., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-01-01
  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: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary