6DBB

Crystal structure of a Putative aldehyde dehydrogenase family protein Burkholderia cenocepacia J2315 in complex with partially reduced NADH

PDB DOI: https://doi.org/10.2210/pdb6DBB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-05-02 Released: 2018-08-29
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.189 (Depositor), 0.189 (DCC)
R-Value Work:
0.147 (Depositor), 0.149 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a Putative aldehyde dehydrogenase family protein Burkholderia cenocepacia J2315 in complex with partially reduced NADH

Abendroth, J., Mayclin, S.J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 170.63 kDa
Atom Count: 12,875
Modelled Residue Count: 1,509
Deposited Residue Count: 1,533
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aldehyde dehydrogenase family protein	A, B, C	511	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAM2468
UniProt
Find proteins for B4EIN4 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EIN4 Go to UniProtKB: B4EIN4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EIN4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAX Query on NAX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth C]	E [auth A], P [auth B], Z [auth C]	BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₃₁ N₇ O₁₅ P₂ IDBZKGQRLBFUFQ-VPHRTNKSSA-N		Interactions Focus chain E [auth A] Focus chain P [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain P [auth B] Focus chain Z [auth C]
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain D [auth A] SDF format, chain O [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B]	D [auth A], O [auth B], Y [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain O [auth B] Focus chain Y [auth C] Interactions & Density Focus chain D [auth A] Focus chain O [auth B] Focus chain Y [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain BA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth C] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.189 (Depositor), 0.189 (DCC)
R-Value Work: 0.147 (Depositor), 0.149 (DCC)
R-Value Observed: 0.148 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36dbb

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.67	α = 90
b = 124.98	β = 90
c = 246.2	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-29

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-08-29
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary