5UNL | pdb_00005unl

Crystal structure of a D-beta-hydroxybutyrate dehydrogenase from Burkholderia multivorans

PDB DOI: https://doi.org/10.2210/pdb5UNL/pdb

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

Deposited: 2017-01-31 Released: 2017-02-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.208 (Depositor), 0.209 (DCC)
R-Value Work:
0.175 (Depositor), 0.176 (DCC)
R-Value Observed:
0.176 (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 a D-beta-hydroxybutyrate dehydrogenase from Burkholderia multivorans

Mayclin, S.J., Dranow, D.M., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 115.35 kDa
Atom Count: 8,938
Modeled Residue Count: 1,054
Deposited Residue Count: 1,092
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-ketoacyl-ACP reductase	A, B, C, D	273	Burkholderia multivorans	Mutation(s): 0 Gene Names: WM33_05200

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.208 (Depositor), 0.209 (DCC)
R-Value Work: 0.175 (Depositor), 0.176 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.38	α = 90
b = 132.09	β = 108.68
c = 64.53	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-02-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-02-15
Type: Initial release
Version 1.1: 2023-10-04
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.