5JY1 | pdb_00005jy1

Crystal Structure of putative short-chain dehydrogenase/reductase from Burkholderia xenovorans LB400 bound to NAD

PDB DOI: https://doi.org/10.2210/pdb5JY1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paraburkholderia xenovorans LB400
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-13 Released: 2016-05-25
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:
0.175 (Depositor), 0.180 (DCC)
R-Value Work:
0.146 (Depositor), 0.150 (DCC)
R-Value Observed:
0.147 (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 putative short-chain dehydrogenase/reductase from Burkholderia xenovorans LB400 bound to NAD

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Delker, S.L., Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 122.72 kDa
Atom Count: 9,522
Modeled Residue Count: 1,064
Deposited Residue Count: 1,096
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 short-chain dehydrogenase/reductase	A, B, C, D	274	Paraburkholderia xenovorans LB400	Mutation(s): 0 Gene Names: Bxe_C0591 EC: 1.1.1.100
UniProt
Find proteins for Q13HF0 (Paraburkholderia xenovorans (strain LB400)) Explore Q13HF0 Go to UniProtKB: Q13HF0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13HF0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D]	E [auth A], K [auth B], O [auth C], T [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	G [auth A] I [auth A] M [auth B] P [auth C] S [auth C] G [auth A], I [auth A], M [auth B], P [auth C], S [auth C], W [auth D], X [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D]	H [auth A], J [auth A], N [auth B], Q [auth C], U [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain U [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D]	F [auth A], L [auth B], R [auth C], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.175 (Depositor), 0.180 (DCC)
R-Value Work: 0.146 (Depositor), 0.150 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.41	α = 90
b = 95.7	β = 98.52
c = 84.14	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-05-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-05-25
Type: Initial release
Version 1.1: 2017-05-24
Changes: Database references
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description