2DBY | pdb_00002dby

Crystal structure of the GTP-binding protein YchF in complexed with GDP

• PDB DOI: https://doi.org/10.2210/pdb2DBY/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-12-16 Released: 2006-06-16 
• Deposition Author(s): Kukimoto-Niino, M., Murayama, K., Shirouzu, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of the GTP-binding protein YchF in complexed with GDP

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.

Macromolecule Content 

• Total Structure Weight: 41.24 kDa 
• Atom Count: 3,170 
• Modeled Residue Count: 355 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein	A	368	Thermus thermophilus HB8	Mutation(s): 2
UniProt
Find proteins for Q5SJ29 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ29  Go to UniProtKB:  Q5SJ29

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
FMT	C [auth A], D [auth A], E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.221 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.384	α = 90
b = 133.169	β = 90
c = 46.432	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-16 
Deposition Author(s): Kukimoto-Niino, M., Murayama, K., Shirouzu, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-06-16
  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: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary