4O6R | pdb_00004o6r

Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb4O6R/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-23 Released: 2014-01-22
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.182 (Depositor), 0.191 (DCC)
R-Value Work:
0.151 (Depositor), 0.162 (DCC)
R-Value Observed:
0.152 (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 from Burkholderia cenocepacia

Dranow, D.M., Abendroth, J., Edwards, T.E., Lorimer, D.

To be published.

Macromolecule Content

Total Structure Weight: 216.01 kDa
Atom Count: 17,485
Modeled Residue Count: 1,956
Deposited Residue Count: 1,984
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	496	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAM0469
UniProt
Find proteins for B4EJX1 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EJX1 Go to UniProtKB: B4EJX1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4EJX1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain W [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain W [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], O [auth C], W [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain W [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain U [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	CA [auth D], H [auth A], L [auth B], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain H [auth A] Focus chain L [auth B] Focus chain U [auth C] Interactions & Density Focus chain CA [auth D] Focus chain H [auth A] Focus chain L [auth B] Focus chain U [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain S [auth C] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain S [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain S [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] G [auth A] Q [auth C] R [auth C] AA [auth D], BA [auth D], G [auth A], Q [auth C], R [auth C], S [auth C], T [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain G [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain G [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth C] SDF format, chain X [auth D] SDF format, chain V [auth D] SDF format, chain N [auth C] SDF format, chain M [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain X [auth D] MOL2 format, chain V [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain X [auth D] mmCIF format, chain V [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A] I [auth A] K [auth B] M [auth B] N [auth C] F [auth A], I [auth A], K [auth B], M [auth B], N [auth C], P [auth C], V [auth D], X [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain P [auth C] Focus chain V [auth D] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain P [auth C] Focus chain V [auth D] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.182 (Depositor), 0.191 (DCC)
R-Value Work: 0.151 (Depositor), 0.162 (DCC)
R-Value Observed: 0.152 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.13	α = 90
b = 125.61	β = 90
c = 150.85	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	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: 2014-01-22

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-01-22
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description