5UY7

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, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Crystal structure of a peptidoglycan glycosyltransferase from Burkholderia ambifaria

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35UY7

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

Entry History 

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references