4KUE | pdb_00004kue

Crystal structure of 3-hydroxybutylryl-CoA dehydrogenase from Clostridium butyricum

PDB DOI: https://doi.org/10.2210/pdb4KUE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium butyricum E4 str. BoNT E BL5262
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-22 Released: 2014-05-28
Deposition Author(s): Kim, E.J., Kim, S., Kim, K.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.234 (Depositor), 0.240 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of (S)-3-hydroxybutylryl-CoA dehydrogenase form the n-butanol sysnthesizing bacterium, Clostridium butyricum

Kim, E.J., Kim, S., Kim, K.J.

To be published.

Macromolecule Content

Total Structure Weight: 125.29 kDa
Atom Count: 8,855
Modeled Residue Count: 1,120
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxybutyryl-CoA dehydrogenase	A, B, C, D	288	Clostridium butyricum E4 str. BoNT E BL5262	Mutation(s): 0 Gene Names: hbd, CLP_3850 EC: 1.1.1.157
UniProt
Find proteins for C4IEM5 (Clostridium butyricum E4 str. BoNT E BL5262) Explore C4IEM5 Go to UniProtKB: C4IEM5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4IEM5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.234 (Depositor), 0.240 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.111	α = 90
b = 144.111	β = 90
c = 204.999	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-05-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-28
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 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 R01GM157729.