5DLD

Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from Burkholderia vietnamiensis complexed with UDP-GlcNAc and UDP

PDB DOI: https://doi.org/10.2210/pdb5DLD/pdb

Classification: ISOMERASE
Organism(s): Burkholderia vietnamiensis G4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-04 Released: 2015-09-30
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.159 (Depositor), 0.160 (DCC)
R-Value Work:
0.134 (Depositor), 0.130 (DCC)
R-Value Observed:
0.136 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of a UDP-N-acetylglucosamine 2-epimerase from Burkholderia vietnamiensis complexed with UDP-GlcNAc and UDP

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

To be published.

Macromolecule Content

Total Structure Weight: 47.02 kDa
Atom Count: 3,592
Modelled Residue Count: 379
Deposited Residue Count: 413
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-Acetylglucosamine 2-epimerase	A	413	Burkholderia vietnamiensis G4	Mutation(s): 0 Gene Names: Bcep1808_4142 EC: 5.1.3.14
UniProt
Find proteins for A4JLG9 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JLG9 Go to UniProtKB: A4JLG9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4JLG9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UD1 Query on UD1 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-CFRASDGPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A], G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.159 (Depositor), 0.160 (DCC)
R-Value Work: 0.134 (Depositor), 0.130 (DCC)
R-Value Observed: 0.136 (Depositor)

Diffraction Data: https://doi.org/10.18430/M35DLD

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116	α = 90
b = 81.41	β = 98.03
c = 55.16	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-09-30

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-09-30
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description