5THW | pdb_00005thw

Crystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia multivorans

• PDB DOI: https://doi.org/10.2210/pdb5THW/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia multivorans ATCC 17616
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-30 Released: 2016-11-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia multivorans

Abendroth, J., Delker, S.L., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 188.57 kDa 
• Atom Count: 12,929 
• Modeled Residue Count: 1,647 
• Deposited Residue Count: 1,736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deacylase	A, B, C, D	434	Burkholderia multivorans ATCC 17616	Mutation(s): 0  Gene Names: BMULJ_06149 EC: 3.5.1.87
UniProt
Find proteins for A0A0H3KRF1 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KRF1  Go to UniProtKB:  A0A0H3KRF1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URP	G [auth A], L [auth C]	N-(AMINOCARBONYL)-BETA-ALANINE C4 H8 N2 O3 JSJWCHRYRHKBBW-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], H [auth B], J [auth C], K [auth C], M [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth B], N [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35THW

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.46	α = 90
b = 88.51	β = 90.21
c = 126.44	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary