1V94 | pdb_00001v94

Crystal structure of isocitrate dehydrogenase from Aeropyrum pernix

PDB DOI: https://doi.org/10.2210/pdb1V94/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aeropyrum pernix
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-01-20 Released: 2005-01-25
Deposition Author(s): Jeong, J.-J., Sonoda, T., Fushinobu, S., Shoun, H., Wakagi, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.256 (Depositor), 0.209 (DCC)
R-Value Work:
0.215 (Depositor), 0.217 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of isocitrate dehydrogenase from Aeropyrum pernix

Jeong, J.-J., Sonoda, T., Fushinobu, S., Shoun, H., Wakagi, T.

(2004) Proteins 55: 1087-1089

PubMed: 15146507 Search on PubMed
DOI: https://doi.org/10.1002/prot.20121
Primary Citation Related Structures:
1V94

Organizational Affiliation

Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.

Macromolecule Content

Total Structure Weight: 95.97 kDa
Atom Count: 6,860
Modeled Residue Count: 852
Deposited Residue Count: 870
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
isocitrate dehydrogenase	A, B	435	Aeropyrum pernix	Mutation(s): 0 Gene Names: APE0689 EC: 1.1.1.42
UniProt
Find proteins for Q9YE81 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YE81 Go to UniProtKB: Q9YE81
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9YE81
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.256 (Depositor), 0.209 (DCC)
R-Value Work: 0.215 (Depositor), 0.217 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.863	α = 90
b = 107.863	β = 90
c = 172.858	γ = 90

Software Package:

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

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: 2023-10-25
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-10-30
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.