Macromolecule Content

Total Structure Weight: 119.53 kDa
Atom Count: 9356
Modelled Residue Count: 1031
Deposited Residue Count: 1060
Unique protein chains: 1

5U9P

Crystal structure of a gluconate 5-dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP and tartrate

DOI: 10.2210/pdb5U9P/pdb

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

Deposited: 2016-12-17 Released: 2017-01-18
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: 0.164
R-Value Work: 0.136
R-Value Observed: 0.136

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of a gluconate 5-dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP and tartrate

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

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gluconate 5-dehydrogenase	A, B, C, D	265	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: idnO, BCAL3386 EC: 1.1.1.69
Find proteins for B4EEX4 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EEX4 Go to UniProtKB: B4EEX4
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain K [B] SDF format, chain Q [C] SDF format, chain W [D] MOL2 format, chain E [A] MOL2 format, chain K [B] MOL2 format, chain Q [C] MOL2 format, chain W [D]	A, B, C, D	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Ligand Interaction
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] SDF format, chain L [B] SDF format, chain M [B] SDF format, chain R [C] SDF format, chain S [C] SDF format, chain X [D] SDF format, chain Y [D] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain L [B] MOL2 format, chain M [B] MOL2 format, chain R [C] MOL2 format, chain S [C] MOL2 format, chain X [D] MOL2 format, chain Y [D]	A, B, C, D	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [A] SDF format, chain I [A] SDF format, chain J [A] SDF format, chain N [B] SDF format, chain O [B] SDF format, chain P [B] SDF format, chain T [C] SDF format, chain U [C] SDF format, chain V [C] SDF format, chain Z [D] MOL2 format, chain H [A] MOL2 format, chain I [A] MOL2 format, chain J [A] MOL2 format, chain N [B] MOL2 format, chain O [B] MOL2 format, chain P [B] MOL2 format, chain T [C] MOL2 format, chain U [C] MOL2 format, chain V [C] MOL2 format, chain Z [D]	A, B, C, D	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.164
R-Value Work: 0.136
R-Value Observed: 0.136
Space Group: P 2₁ 2₁ 2₁
Diffraction Data DOI: 10.18430/M35U9P Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.38	α = 90
b = 91.68	β = 90
c = 121.44	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2016-12-17
Released Date: 2017-01-18

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.