6UX3 | pdb_00006ux3

Crystal structure of acetoin dehydrogenase from Enterobacter cloacae

PDB DOI: https://doi.org/10.2210/pdb6UX3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Enterobacter cloacae subsp. cloacae ATCC 13047
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-11-06 Released: 2019-11-20
Deposition Author(s): Chang, C., Skarina, T., Mesa, N., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.176 (Depositor), 0.177 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of acetoin dehydrogenase from Enterobacter cloacae

Chang, C., Skarina, T., Mesa, N., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 109.91 kDa
Atom Count: 7,771
Modeled Residue Count: 988
Deposited Residue Count: 1,028
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetoin dehydrogenase	A, B, C, D	257	Enterobacter cloacae subsp. cloacae ATCC 13047	Mutation(s): 0 Gene Names: ECL_03449
UniProt
Find proteins for A0A0H3CM71 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56)) Explore A0A0H3CM71 Go to UniProtKB: A0A0H3CM71
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3CM71
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth D] MOL2 format, chain F [auth D] mmCIF format, chain F [auth D]	F [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.176 (Depositor), 0.177 (DCC)
R-Value Observed: 0.179 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.07	α = 90
b = 99.836	β = 98.89
c = 82.217	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-11-20

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2019-11-20
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, 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.