3ENK

1.9A crystal structure of udp-glucose 4-epimerase from burkholderia pseudomallei

PDB DOI: https://doi.org/10.2210/pdb3ENK/pdb

Classification: ISOMERASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-25 Released: 2008-10-28
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: 0.245
R-Value Work: 0.194
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

1.9A crystal structure of udp-glucose 4-epimerase from burkholderia pseudomallei

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 77.01 kDa
Atom Count: 5,774
Modelled Residue Count: 679
Deposited Residue Count: 682
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase	A, B	341	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: BURPS1710B_2458, BURPS1710b_3147, galE, MSRB EC: 5.1.3.2
UniProt
Find proteins for Q3JPI3 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JPI3 Go to UniProtKB: Q3JPI3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3JPI3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
UPG Query on UPG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.245
R-Value Work: 0.194
R-Value Observed: 0.197
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.86	α = 90
b = 83.471	β = 96.17
c = 82.576	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-28

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2008-10-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-05-08
Changes: Non-polymer description
Version 1.3: 2017-10-25
Changes: Refinement description
Version 1.4: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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3ENK

1.9A crystal structure of udp-glucose 4-epimerase from burkholderia pseudomallei

1.9A crystal structure of udp-glucose 4-epimerase from burkholderia pseudomallei

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)