5KF0 | pdb_00005kf0

Crystal structure of an Aldedhyde dehydrogenase from Burkholderia vietnamiensis

PDB DOI: https://doi.org/10.2210/pdb5KF0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia vietnamiensis G4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-10 Released: 2016-11-09
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.157 (Depositor), 0.156 (DCC)
R-Value Work:
0.134 (Depositor), 0.134 (DCC)
R-Value Observed:
0.134 (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 an Aldedhyde dehydrogenase from Burkholderia vietnamiensis

Abendroth, J., Fox III, D., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 217.66 kDa
Atom Count: 17,525
Modeled Residue Count: 1,908
Deposited Residue Count: 1,940
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase	A, B, C, D	485	Burkholderia vietnamiensis G4	Mutation(s): 0 Gene Names: Bcep1808_4170
UniProt
Find proteins for A4JLJ7 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JLJ7 Go to UniProtKB: A4JLJ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4JLJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain L [auth B] SDF format, chain E [auth A] SDF format, chain CA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth D]	CA [auth D], E [auth A], L [auth B], U [auth C]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain CA [auth D] Focus chain E [auth A] Focus chain L [auth B] Focus chain U [auth C] Interactions & Density Focus chain CA [auth D] Focus chain E [auth A] Focus chain L [auth B] Focus chain U [auth C]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain N [auth B] SDF format, chain HA [auth D] SDF format, chain G [auth A] SDF format, chain EA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain N [auth B] MOL2 format, chain HA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain N [auth B] mmCIF format, chain HA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth D]	EA [auth D], G [auth A], HA [auth D], N [auth B], W [auth C]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain EA [auth D] Focus chain G [auth A] Focus chain HA [auth D] Focus chain N [auth B] Focus chain W [auth C] Interactions & Density Focus chain EA [auth D] Focus chain G [auth A] Focus chain HA [auth D] Focus chain N [auth B] Focus chain W [auth C]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain GA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] GA [auth D] I [auth A] J [auth A] AA [auth D], BA [auth D], GA [auth D], I [auth A], J [auth A], K [auth A], O [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], Y [auth C], Z [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain FA [auth D] SDF format, chain DA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain DA [auth D]	DA [auth D] FA [auth D] H [auth A] M [auth B] P [auth B] DA [auth D], FA [auth D], H [auth A], M [auth B], P [auth B], V [auth C], X [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain FA [auth D] Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain FA [auth D] Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth B] Focus chain V [auth C] Focus chain X [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.157 (Depositor), 0.156 (DCC)
R-Value Work: 0.134 (Depositor), 0.134 (DCC)
R-Value Observed: 0.134 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.64	α = 90
b = 145.08	β = 90
c = 170.03	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description