5JYD | pdb_00005jyd

Crystal Structure of a Putative Short Chain Dehydrogenase from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb5JYD/pdb

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

Deposited: 2016-05-13 Released: 2016-06-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.174 (Depositor), 0.182 (DCC)
R-Value Work:
0.141 (Depositor), 0.152 (DCC)
R-Value Observed:
0.142 (Depositor)

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 Short Chain Dehydrogenase from Burkholderia cenocepacia

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Yano, J.Y., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 273.68 kDa
Atom Count: 19,905
Modeled Residue Count: 2,330
Deposited Residue Count: 2,480
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short chain dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	310	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAL1205
UniProt
Find proteins for B4EEE3 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EEE3 Go to UniProtKB: B4EEE3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4EEE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain BC [auth H] SDF format, chain IB [auth F] SDF format, chain KA [auth D] SDF format, chain RB [auth G] SDF format, chain S [auth B] SDF format, chain VA [auth E] SDF format, chain I [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain BC [auth H] MOL2 format, chain IB [auth F] MOL2 format, chain KA [auth D] MOL2 format, chain RB [auth G] MOL2 format, chain S [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain I [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain BC [auth H] mmCIF format, chain IB [auth F] mmCIF format, chain KA [auth D] mmCIF format, chain RB [auth G] mmCIF format, chain S [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain I [auth A]	BA [auth C] BC [auth H] I [auth A] IB [auth F] KA [auth D] BA [auth C], BC [auth H], I [auth A], IB [auth F], KA [auth D], RB [auth G], S [auth B], VA [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain BA [auth C] Focus chain BC [auth H] Focus chain I [auth A] Focus chain IB [auth F] Focus chain KA [auth D] Focus chain RB [auth G] Focus chain S [auth B] Focus chain VA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain BC [auth H] Focus chain I [auth A] Focus chain IB [auth F] Focus chain KA [auth D] Focus chain RB [auth G] Focus chain S [auth B] Focus chain VA [auth E]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain CB [auth E] SDF format, chain DA [auth C] SDF format, chain DB [auth E] SDF format, chain DC [auth H] SDF format, chain EA [auth C] SDF format, chain EB [auth E] SDF format, chain EC [auth H] SDF format, chain FA [auth C] SDF format, chain FC [auth H] SDF format, chain GA [auth C] SDF format, chain GC [auth H] SDF format, chain HA [auth C] SDF format, chain HC [auth H] SDF format, chain IA [auth C] SDF format, chain IC [auth H] SDF format, chain K [auth A] SDF format, chain KB [auth F] SDF format, chain L [auth A] SDF format, chain LB [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain MB [auth F] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain NB [auth F] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain OB [auth F] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain PB [auth F] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain QB [auth F] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TB [auth G] SDF format, chain U [auth B] SDF format, chain UB [auth G] SDF format, chain V [auth B] SDF format, chain VB [auth G] SDF format, chain W [auth B] SDF format, chain WB [auth G] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain XB [auth G] SDF format, chain Y [auth B] SDF format, chain YA [auth E] SDF format, chain YB [auth G] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth E] MOL2 format, chain DC [auth H] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth E] MOL2 format, chain EC [auth H] MOL2 format, chain FA [auth C] MOL2 format, chain FC [auth H] MOL2 format, chain GA [auth C] MOL2 format, chain GC [auth H] MOL2 format, chain HA [auth C] MOL2 format, chain HC [auth H] MOL2 format, chain IA [auth C] MOL2 format, chain IC [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain OB [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain QB [auth F] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TB [auth G] MOL2 format, chain U [auth B] MOL2 format, chain UB [auth G] MOL2 format, chain V [auth B] MOL2 format, chain VB [auth G] MOL2 format, chain W [auth B] MOL2 format, chain WB [auth G] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain XB [auth G] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain YB [auth G] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain CB [auth E] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth E] mmCIF format, chain DC [auth H] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth E] mmCIF format, chain EC [auth H] mmCIF format, chain FA [auth C] mmCIF format, chain FC [auth H] mmCIF format, chain GA [auth C] mmCIF format, chain GC [auth H] mmCIF format, chain HA [auth C] mmCIF format, chain HC [auth H] mmCIF format, chain IA [auth C] mmCIF format, chain IC [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KB [auth F] mmCIF format, chain L [auth A] mmCIF format, chain LB [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth F] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain NB [auth F] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain OB [auth F] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain PB [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain QB [auth F] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TB [auth G] mmCIF format, chain U [auth B] mmCIF format, chain UB [auth G] mmCIF format, chain V [auth B] mmCIF format, chain VB [auth G] mmCIF format, chain W [auth B] mmCIF format, chain WB [auth G] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain XB [auth G] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain YB [auth G] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth E]	AA [auth B] AB [auth E] BB [auth E] CB [auth E] DA [auth C] AA [auth B], AB [auth E], BB [auth E], CB [auth E], DA [auth C], DB [auth E], DC [auth H], EA [auth C], EB [auth E], EC [auth H], FA [auth C], FC [auth H], GA [auth C], GC [auth H], HA [auth C], HC [auth H], IA [auth C], IC [auth H], K [auth A], KB [auth F], L [auth A], LB [auth F], M [auth A], MA [auth D], MB [auth F], N [auth A], NA [auth D], NB [auth F], O [auth A], OA [auth D], OB [auth F], P [auth A], PA [auth D], PB [auth F], Q [auth A], QA [auth D], QB [auth F], RA [auth D], SA [auth D], TB [auth G], U [auth B], UB [auth G], V [auth B], VB [auth G], W [auth B], WB [auth G], X [auth B], XA [auth E], XB [auth G], Y [auth B], YA [auth E], YB [auth G], Z [auth B], ZA [auth E]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DA [auth C] Focus chain DB [auth E] Focus chain DC [auth H] Focus chain EA [auth C] Focus chain EB [auth E] Focus chain EC [auth H] Focus chain FA [auth C] Focus chain FC [auth H] Focus chain GA [auth C] Focus chain GC [auth H] Focus chain HA [auth C] Focus chain HC [auth H] Focus chain IA [auth C] Focus chain IC [auth H] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QB [auth F] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TB [auth G] Focus chain U [auth B] Focus chain UB [auth G] Focus chain V [auth B] Focus chain VB [auth G] Focus chain W [auth B] Focus chain WB [auth G] Focus chain X [auth B] Focus chain XA [auth E] Focus chain XB [auth G] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain YB [auth G] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DA [auth C] Focus chain DB [auth E] Focus chain DC [auth H] Focus chain EA [auth C] Focus chain EB [auth E] Focus chain EC [auth H] Focus chain FA [auth C] Focus chain FC [auth H] Focus chain GA [auth C] Focus chain GC [auth H] Focus chain HA [auth C] Focus chain HC [auth H] Focus chain IA [auth C] Focus chain IC [auth H] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LB [auth F] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth D] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain QB [auth F] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TB [auth G] Focus chain U [auth B] Focus chain UB [auth G] Focus chain V [auth B] Focus chain VB [auth G] Focus chain W [auth B] Focus chain WB [auth G] Focus chain X [auth B] Focus chain XA [auth E] Focus chain XB [auth G] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain YB [auth G] Focus chain Z [auth B] Focus chain ZA [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain ZB [auth G] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain ZB [auth G] mmCIF format, chain FB [auth E] mmCIF format, chain GB [auth E] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain ZB [auth G]	FB [auth E], GB [auth E], TA [auth D], UA [auth D], ZB [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FB [auth E] Focus chain GB [auth E] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain ZB [auth G] Interactions & Density Focus chain FB [auth E] Focus chain GB [auth E] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain ZB [auth G]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain CC [auth H] SDF format, chain J [auth A] SDF format, chain JB [auth F] SDF format, chain LA [auth D] SDF format, chain SB [auth G] SDF format, chain T [auth B] SDF format, chain WA [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain CC [auth H] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth F] MOL2 format, chain LA [auth D] MOL2 format, chain SB [auth G] MOL2 format, chain T [auth B] MOL2 format, chain WA [auth E] mmCIF format, chain CA [auth C] mmCIF format, chain CC [auth H] mmCIF format, chain J [auth A] mmCIF format, chain JB [auth F] mmCIF format, chain LA [auth D] mmCIF format, chain SB [auth G] mmCIF format, chain T [auth B] mmCIF format, chain WA [auth E]	CA [auth C] CC [auth H] J [auth A] JB [auth F] LA [auth D] CA [auth C], CC [auth H], J [auth A], JB [auth F], LA [auth D], SB [auth G], T [auth B], WA [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain CC [auth H] Focus chain J [auth A] Focus chain JB [auth F] Focus chain LA [auth D] Focus chain SB [auth G] Focus chain T [auth B] Focus chain WA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain CC [auth H] Focus chain J [auth A] Focus chain JB [auth F] Focus chain LA [auth D] Focus chain SB [auth G] Focus chain T [auth B] Focus chain WA [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AC [auth G] SDF format, chain JA [auth C] SDF format, chain R [auth A] SDF format, chain HB [auth E] MOL2 format, chain AC [auth G] MOL2 format, chain JA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain HB [auth E] mmCIF format, chain AC [auth G] mmCIF format, chain JA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain HB [auth E]	AC [auth G], HB [auth E], JA [auth C], R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AC [auth G] Focus chain HB [auth E] Focus chain JA [auth C] Focus chain R [auth A] Interactions & Density Focus chain AC [auth G] Focus chain HB [auth E] Focus chain JA [auth C] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.174 (Depositor), 0.182 (DCC)
R-Value Work: 0.141 (Depositor), 0.152 (DCC)
R-Value Observed: 0.142 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.8	α = 90
b = 107.82	β = 97.63
c = 117.69	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-06-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-06-08
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2025-10-22
Changes: Database references, Structure summary