3RU7

Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase

PDB DOI: https://doi.org/10.2210/pdb3RU7/pdb

Classification: ISOMERASE
Organism(s): Plesiomonas shigelloides
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-05-04 Released: 2011-05-25
Deposition Author(s): Bhatt, V.S., Guan, W., Wang, P.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.270
R-Value Work: 0.217
R-Value Observed: 0.220

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase

Bhatt, V.S., Guan, W., G Wang, P.

To be published.

Macromolecule Content

Total Structure Weight: 162.38 kDa
Atom Count: 11,120
Modelled Residue Count: 1,344
Deposited Residue Count: 1,404
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WbgU	A, B, C, D	351	Plesiomonas shigelloides	Mutation(s): 0 Gene Names: wbgU EC: 5.1.3.7
UniProt
Find proteins for Q7BJX9 (Plesiomonas shigelloides) Explore Q7BJX9 Go to UniProtKB: Q7BJX9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7BJX9
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 E [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D]	E [auth A], J [auth B], N [auth C], S [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C]	M [auth B], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain P [auth C] Interactions & Density Focus chain M [auth B] Focus chain P [auth C]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain R [auth D]	F [auth A], R [auth D]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain R [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C]	G [auth A], H [auth A], L [auth B], Q [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C]
UNL Query on UNL Download Ideal Coordinates CCD File	I [auth A], K [auth B], O [auth C], T [auth D]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.270
R-Value Work: 0.217
R-Value Observed: 0.220
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.73	α = 90
b = 77.73	β = 90
c = 224.54	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-05-25

Deposition Author(s):

Bhatt, V.S.

Guan, W.

Wang, P.G.

Revision History (Full details and data files)

Version 1.0: 2011-05-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description