2DWQ | pdb_00002dwq

Thermus thermophilus YchF GTP-binding protein

• PDB DOI: https://doi.org/10.2210/pdb2DWQ/pdb

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


• Deposited: 2006-08-16 Released: 2007-02-16 
• Deposition Author(s): Kukimoto-Niino, M., Murayama, K., Shorouzu, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.281 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Thermus thermophilus YchF GTP-binding protein

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

Macromolecule Content 

• Total Structure Weight: 81.13 kDa 
• Atom Count: 5,410 
• Modeled Residue Count: 691 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein	A, B	368	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ29 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ29  Go to UniProtKB:  Q5SJ29

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.281 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.94	α = 80.11
b = 54.357	β = 76.46
c = 92.585	γ = 73.12

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: 2007-02-16 
Deposition Author(s): Kukimoto-Niino, M., Murayama, K., Shorouzu, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-02-16
  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