2E87

Crystal structure of hypothetical GTP-binding protein PH1320 from Pyrococcus horikoshii OT3, in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb2E87/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-01-19 Released: 2007-07-24 
• Deposition Author(s): Kukimoto-Niino, M., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.255 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

Crystal structure of hypothetical GTP-binding protein PH1320 from Pyrococcus horikoshii OT3, in complex with GDP

Kukimoto-Niino, M., Bessho, M., Shirouzu, M., 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: 42.53 kDa 
• Atom Count: 3,021 
• Modelled Residue Count: 356 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein PH1320	A	357	Pyrococcus horikoshii OT3	Mutation(s): 3
UniProt
Find proteins for O59046 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O59046  Go to UniProtKB:  O59046

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	F [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.35 Å
• R-Value Free: 0.255 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.253	α = 90
b = 99.191	β = 90
c = 126.135	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-24 
Deposition Author(s): Kukimoto-Niino, M., Bessho, Y., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-07-24
  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