3RU7 | pdb_00003ru7

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 (Depositor), 0.270 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 1,344
Deposited Residue Count: 1,404
Unique protein chains: 1

Macromolecules

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(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 S [auth D] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C]	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 R [auth D] SDF format, chain F [auth A] MOL2 format, chain R [auth D] MOL2 format, chain F [auth A] mmCIF format, chain R [auth D] mmCIF format, chain F [auth A]	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 Q [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	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 (Depositor), 0.270 (DCC)
R-Value Work: 0.217 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

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

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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