4WEO | pdb_00004weo

Crystal Structure of a Putative acetoin(Diacetyl) Reductase Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb4WEO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-09-10 Released: 2014-09-24
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.160 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a Putative acetoin(Diacetyl) Reductase Burkholderia cenocepacia

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Dranow, D.M., Fairman, J.W., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 114 kDa
Atom Count: 7,731
Modeled Residue Count: 958
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acetoin(Diacetyl) reductase	A, B, C, D	266	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: budC, BCAL1912 EC: 1.1.1.5
UniProt
Find proteins for B4EAZ8 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EAZ8 Go to UniProtKB: B4EAZ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EAZ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain K [auth C] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C]	K [auth C], O [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain K [auth C] Focus chain O [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth C] E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], M [auth D], N [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain L [auth C]	L [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain L [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.160 (DCC)
R-Value Observed: 0.156 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34WEO

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.71	α = 90
b = 85.49	β = 92.27
c = 76.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
XSCALE	data scaling
BALBES	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-09-24
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description