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.

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 1VAJ

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.20315
Primary Citation Related Structures:
1VAJ

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O57770
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

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Entry History

Deposition Data

Released Date: 2005-01-25

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.