5UY7 | pdb_00005uy7

Crystal structure of a peptidoglycan glycosyltransferase from Burkholderia ambifaria

PDB DOI: https://doi.org/10.2210/pdb5UY7/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia ambifaria MC40-6
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-23 Released: 2017-03-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.187 (Depositor), 0.189 (DCC)
R-Value Work:
0.159 (Depositor), 0.160 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5UY7

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a peptidoglycan glycosyltransferase from Burkholderia ambifaria

Edwards, T.E., Abendroth, J., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 63.04 kDa
Atom Count: 2,648
Modeled Residue Count: 316
Deposited Residue Count: 579
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan glycosyltransferase	A	579	Burkholderia ambifaria MC40-6	Mutation(s): 0 Gene Names: BamMC406_0482 EC: 2.4.1.129 (PDB Primary Data), 3.4.16.4 (UniProt)
UniProt
Find proteins for B1YSR8 (Burkholderia ambifaria (strain MC40-6)) Explore B1YSR8 Go to UniProtKB: B1YSR8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1YSR8
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 F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.187 (Depositor), 0.189 (DCC)
R-Value Work: 0.159 (Depositor), 0.160 (DCC)
R-Value Observed: 0.160 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.8	α = 90
b = 74.31	β = 90
c = 137.17	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-03-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-03-08
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references
Version 1.2: 2025-10-22
Changes: Database references, Structure summary

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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.