2IT2

Structure of PH1069 protein from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb2IT2/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-18 Released: 2007-11-13 
• Deposition Author(s): Lokanath, N.K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 

Starting Model: experimental

Literature

Structure of PH1069 protein from Pyrococcus horikoshii

Lokanath, N.K., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.09 kDa 
• Atom Count: 3,446 
• Modelled Residue Count: 385 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0130 protein PH1069	A, B	200	Pyrococcus horikoshii	Mutation(s): 0  EC: 2.1.1.282
UniProt
Find proteins for O58796 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58796  Go to UniProtKB:  O58796

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.250 
• R-Value Observed: 0.250 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.428	α = 104.6
b = 53.902	β = 102.9
c = 53.212	γ = 109.3

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Lokanath, N.K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection