4TRR

Crystal structure of a putative Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315

PDB DOI: https://doi.org/10.2210/pdb4TRR/pdb

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

Deposited: 2014-06-17 Released: 2014-08-06
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.222
R-Value Work: 0.183
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Lukacs, C., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 228.38 kDa
Atom Count: 15,759
Modelled Residue Count: 2,006
Deposited Residue Count: 2,152
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 D-beta-hydroxybutyrate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	269	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAM0022
UniProt
Find proteins for B4EG08 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EG08 Go to UniProtKB: B4EG08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EG08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth H]	I [auth A] K [auth B] L [auth C] N [auth D] P [auth E] I [auth A], K [auth B], L [auth C], N [auth D], P [auth E], R [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth D] SDF format, chain O [auth D] SDF format, chain Q [auth F] MOL2 format, chain J [auth A] MOL2 format, chain M [auth D] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth F]	J [auth A], M [auth D], O [auth D], Q [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth D] Focus chain O [auth D] Focus chain Q [auth F] Interactions & Density Focus chain J [auth A] Focus chain M [auth D] Focus chain O [auth D] Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.222
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m34trr

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.22	α = 90
b = 91.95	β = 92.94
c = 116.56	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2017-11-22
Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description

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Help and Resources

4TRR

Crystal structure of a putative Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315

Crystal structure of a putative Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)