5W15

Crystal structure of an alpha/beta hydrolase fold protein from Burkholderia ambifaria.

• PDB DOI: https://doi.org/10.2210/pdb5W15/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia ambifaria MC40-6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-01 Released: 2017-06-14 
• Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.188 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 

Literature

Crystal structure of an alpha/beta hydrolase fold protein from Burkholderia ambifaria.

Irwin, R.M., Mayclin, S.J., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 123.63 kDa 
• Atom Count: 10,072 
• Modelled Residue Count: 1,080 
• Deposited Residue Count: 1,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase fold protein	A, B, C, D	275	Burkholderia ambifaria MC40-6	Mutation(s): 0  Gene Names: BamMC406_3075
UniProt
Find proteins for B1YPY7 (Burkholderia ambifaria (strain MC40-6)) Explore B1YPY7  Go to UniProtKB:  B1YPY7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	L [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.188 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M35W15

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.07	α = 90
b = 143.59	β = 111.34
c = 75.85	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
PHENIX	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description