5JSC | pdb_00005jsc

Crystal structure of a Putative acyl-CoA dehydrogenase from Burkholderia xenovorans

PDB DOI: https://doi.org/10.2210/pdb5JSC/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paraburkholderia xenovorans LB400
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-07 Released: 2016-06-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.160 (Depositor), 0.161 (DCC)
R-Value Work:
0.130 (Depositor), 0.131 (DCC)
R-Value Observed:
0.130 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a Putative acyl-CoA dehydrogenase from Burkholderia xenovorans

Abendroth, J., Delker, S.L., Lorimer, D.D., Edewards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 179.7 kDa
Atom Count: 13,877
Modeled Residue Count: 1,551
Deposited Residue Count: 1,640
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acyl-CoA dehydrogenase	A, B, C, D	410	Paraburkholderia xenovorans LB400	Mutation(s): 0 Gene Names: Bxe_B0278 EC: 1.3.8
UniProt
Find proteins for Q13JS1 (Paraburkholderia xenovorans (strain LB400)) Explore Q13JS1 Go to UniProtKB: Q13JS1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13JS1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain M [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain M [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain M [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], M [auth C], T [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain T [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain L [auth B]	K [auth B] L [auth B] P [auth C] Q [auth C] R [auth C] K [auth B], L [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], W [auth D], X [auth D], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain V [auth D] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain V [auth D] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain V [auth D] mmCIF format, chain G [auth A]	G [auth A], J [auth B], O [auth C], V [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain V [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain U [auth D] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain U [auth D] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], N [auth C], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.160 (Depositor), 0.161 (DCC)
R-Value Work: 0.130 (Depositor), 0.131 (DCC)
R-Value Observed: 0.130 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.3	α = 90
b = 73.75	β = 99.66
c = 149.49	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-06-08
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description