3VPX

Crystal structure of leucine dehydrogenase from a psychrophilic bacterium Sporosarcina psychrophila.

PDB DOI: https://doi.org/10.2210/pdb3VPX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sporosarcina psychrophila
Mutation(s): No

Deposited: 2012-03-14 Released: 2013-02-06
Deposition Author(s): Zhao, Y., Wakamatsu, T., Doi, K., Sakuraba, H., Ohshima, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.290
R-Value Work: 0.243

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A psychrophilic leucine dehydrogenase from Sporosarcina psychrophila: Purification, characterization, gene sequencing and crystal structure analysis

Zhao, Y., Wakamatsu, T., Doi, K., Sakuraba, H., Ohshima, T.

(2012) J Mol Catal B Enzym 83: 65-72

DOI: https://doi.org/10.1016/j.molcatb.2012.06.018

Macromolecule Content

Total Structure Weight: 78.77 kDa
Atom Count: 5,517
Modelled Residue Count: 715
Deposited Residue Count: 728
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine dehydrogenase	A, B	364	Sporosarcina psychrophila	Mutation(s): 0 EC: 1.4.1.9
UniProt
Find proteins for I0IJU1 (Sporosarcina psychrophila) Explore I0IJU1 Go to UniProtKB: I0IJU1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I0IJU1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.290
R-Value Work: 0.243
Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.589	α = 90
b = 135.589	β = 90
c = 123.553	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-06
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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 R01GM133198.