1VAJ | pdb_00001vaj

Crystal Structure of Uncharacterized Protein PH0010 From Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb1VAJ/pdb

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


• Deposited: 2004-02-17 Released: 2005-01-25 
• Deposition Author(s): Tajika, Y., Sakai, N., Tamura, T., Yao, M., Watanabe, N., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.232 (Depositor) 
• R-Value Work: 
  0.202 (Depositor) 

Literature

Crystal structure of PH0010 from Pyrococcus horikoshii, which is highly homologous to human AMMECR 1C-terminal region

Tajika, Y., Sakai, N., Tamura, T., Yao, M., Watanabe, N., Tanaka, I.

(2005) Proteins 58: 501-503

• PubMed: 15558565 
• DOI: https://doi.org/10.1002/prot.20315
• Primary Citation of Related Structures:  
  1VAJ

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Organizational Affiliation: 

Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.86 kDa 
• Atom Count: 1,811 
• Modelled Residue Count: 203 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein PH0010	A	214	Pyrococcus horikoshii	Mutation(s): 3  Gene Names: PH0010
UniProt
Find proteins for O57770 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57770  Go to UniProtKB:  O57770

Small Molecules

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: 1.82 Å
• R-Value Free:  0.232 (Depositor) 
• R-Value Work:  0.202 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.672	α = 90
b = 67.223	β = 104.27
c = 58.728	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-25 
Deposition Author(s): Tajika, Y., Sakai, N., Tamura, T., Yao, M., Watanabe, N., Tanaka, I.

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Structure summary