4YWE | pdb_00004ywe

Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb4YWE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-03-20 Released: 2015-04-08
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:
0.243 (Depositor), 0.240 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a Putative Aldehyde Dehydrogenase from Burkholderia cenocepacia

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Dranow, D.M., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 413.03 kDa
Atom Count: 31,507
Modeled Residue Count: 3,806
Deposited Residue Count: 3,896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aldehyde dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	487	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAL2623
UniProt
Find proteins for B4E8B7 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4E8B7 Go to UniProtKB: B4E8B7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4E8B7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain MA [auth H] SDF format, chain M [auth B] SDF format, chain LA [auth H] SDF format, chain KA [auth H] SDF format, chain JA [auth H] SDF format, chain I [auth A] SDF format, chain GA [auth G] SDF format, chain FA [auth G] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain CA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain MA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain LA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain MA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain LA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth G]	CA [auth G] DA [auth G] EA [auth G] FA [auth G] GA [auth G] CA [auth G], DA [auth G], EA [auth G], FA [auth G], GA [auth G], I [auth A], JA [auth H], KA [auth H], LA [auth H], M [auth B], MA [auth H], N [auth B], P [auth C], Q [auth C], X [auth F], Y [auth F], Z [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth B] Focus chain MA [auth H] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain M [auth B] Focus chain MA [auth H] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain NA [auth H] SDF format, chain K [auth A] SDF format, chain IA [auth G] SDF format, chain HA [auth G] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain W [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain W [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] HA [auth G] IA [auth G] K [auth A] AA [auth F], BA [auth F], HA [auth G], IA [auth G], K [auth A], NA [auth H], O [auth B], S [auth C], T [auth D], U [auth D], W [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain K [auth A] Focus chain NA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain K [auth A] Focus chain NA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain R [auth C] SDF format, chain L [auth A] SDF format, chain J [auth A] MOL2 format, chain V [auth E] MOL2 format, chain R [auth C] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] mmCIF format, chain V [auth E] mmCIF format, chain R [auth C] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A]	J [auth A], L [auth A], R [auth C], V [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth A] Focus chain R [auth C] Focus chain V [auth E] Interactions & Density Focus chain J [auth A] Focus chain L [auth A] Focus chain R [auth C] Focus chain V [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.243 (Depositor), 0.240 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34YWE

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.32	α = 89.12
b = 93.07	β = 78.55
c = 139.43	γ = 89.85

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-04-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-04-08
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy