2DVK | pdb_00002dvk

Crystal Structure of Hypothetical protein from Aeropyrum pernix

PDB DOI: https://doi.org/10.2210/pdb2DVK/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Aeropyrum pernix
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-07-31 Released: 2007-01-31
Deposition Author(s): Lokanath, N.K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.249 (Depositor), 0.251 (DCC)
R-Value Work:
0.234 (Depositor), 0.235 (DCC)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2DVK

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Hypothetical protein from Aeropyrum pernix

Lokanath, N.K., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 21.02 kDa
Atom Count: 1,496
Modeled Residue Count: 166
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0130 protein APE0816	A	188	Aeropyrum pernix	Mutation(s): 0 EC: 2.1.1.282
UniProt
Find proteins for Q9YDV3 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YDV3 Go to UniProtKB: Q9YDV3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9YDV3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.249 (Depositor), 0.251 (DCC)
R-Value Work: 0.234 (Depositor), 0.235 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.87	α = 90
b = 70.232	β = 90
c = 91.579	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-01-31

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-01-31
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-10-23
Changes: Data collection, Database references, 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.