2EHD | pdb_00002ehd

Crystal Structure Analysis of Oxidoreductase

PDB DOI: https://doi.org/10.2210/pdb2EHD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-06 Released: 2008-03-11
Deposition Author(s): Kamiya, N., Hikima, T., Ebihara, A., Inoue, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.255 (Depositor), 0.251 (DCC)
R-Value Work:
0.226 (Depositor), 0.224 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure analysis of putative oxidoreductase from Thermus thermophilus HB8

Kamiya, N., Hikima, T., Ebihara, A., Inoue, Y.

To be published.

Macromolecule Content

Total Structure Weight: 49.16 kDa
Atom Count: 3,193
Modeled Residue Count: 420
Deposited Residue Count: 468
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, short-chain dehydrogenase/reductase family	A, B	234	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SK86 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SK86 Go to UniProtKB: Q5SK86
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SK86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.255 (Depositor), 0.251 (DCC)
R-Value Work: 0.226 (Depositor), 0.224 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.02	α = 90
b = 104.02	β = 90
c = 105.93	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-03-11

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-03-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.2: 2014-11-12
Changes: Structure summary
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.