5EZ3 | pdb_00005ez3

Crystal structure Acyl-CoA dehydrogenase from Brucella melitensis in complex with FAD

PDB DOI: https://doi.org/10.2210/pdb5EZ3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brucella melitensis bv. 1 str. 16M
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-11-26 Released: 2015-12-09
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.178 (Depositor), 0.180 (DCC)
R-Value Work:
0.145 (Depositor), 0.150 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure Acyl-CoA dehydrogenase from Brucella melitensis in complex with FAD

Abendroth, J., Sankaran, B., Lorimer, D., Edwards, T.

To be published.

Macromolecule Content

Total Structure Weight: 256.05 kDa
Atom Count: 18,169
Modeled Residue Count: 2,163
Deposited Residue Count: 2,292
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA dehydrogenase	A, B, C, D	573	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0 Gene Names: BMEII0671 EC: 1.3.8
UniProt
Find proteins for Q8YC61 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YC61 Go to UniProtKB: Q8YC61
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8YC61
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 E [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D]	E [auth A], I [auth B], N [auth C], S [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain S [auth D]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	H [auth A] L [auth B] M [auth B] Q [auth C] R [auth C] H [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], V [auth D], W [auth D]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D]	G [auth A], K [auth B], P [auth C], U [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D]	F [auth A], J [auth B], O [auth C], T [auth D]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.178 (Depositor), 0.180 (DCC)
R-Value Work: 0.145 (Depositor), 0.150 (DCC)
R-Value Observed: 0.146 (Depositor)

Diffraction Data: https://doi.org/10.18430/M35EZ3

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.92	α = 90
b = 141.25	β = 90
c = 193.22	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-12-09

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-12-09
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description