4XYW | pdb_00004xyw

Glycosyltransferases WbnH

PDB DOI: https://doi.org/10.2210/pdb4XYW/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-02-03 Released: 2016-02-10
Deposition Author(s): Li, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.240 (Depositor), 0.246 (DCC)
R-Value Work:
0.205 (Depositor), 0.215 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4XYW

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

Literature

Glycosyltransferases WbnH

Li, F.

To be published.

Macromolecule Content

Total Structure Weight: 38.41 kDa
Atom Count: 2,587
Modeled Residue Count: 324
Deposited Residue Count: 338
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-antigen biosynthesis glycosyltransferase WbnH	A	338	Escherichia coli	Mutation(s): 1 Gene Names: wbnH, wbwH, wcmA EC: 2.4.1.306
UniProt
Find proteins for P0DMP6 (Escherichia coli) Explore P0DMP6 Go to UniProtKB: P0DMP6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DMP6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240 (Depositor), 0.246 (DCC)
R-Value Work: 0.205 (Depositor), 0.215 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.311	α = 90
b = 114.311	β = 90
c = 183.479	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-02-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-02-10
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.