1WU8 | pdb_00001wu8

Crystal structure of project PH0463 from Pyrococcus horikoshii OT3

• PDB DOI: https://doi.org/10.2210/pdb1WU8/pdb

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


• Deposited: 2004-12-02 Released: 2005-11-29 
• Deposition Author(s): Shimizu, K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.228 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of project ID PH0463 from Pyrococcus horikoshii OT3

Shimizu, K., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 87.6 kDa 
• Atom Count: 6,384 
• Modeled Residue Count: 768 
• Deposited Residue Count: 768 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein PH0463	A, B, C	256	Pyrococcus horikoshii OT3	Mutation(s): 6  EC: 3.13.2.3
UniProt
Find proteins for O58212 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58212  Go to UniProtKB:  O58212

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN	D [auth A], E [auth B], F [auth C]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-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: 2.60 Å
• R-Value Free:  0.228 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.756	α = 90
b = 138.756	β = 90
c = 139.691	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: 2005-11-29 
Deposition Author(s): Shimizu, K., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-11-29
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary