4GXW | pdb_00004gxw

Crystal structure of a cog1816 amidohydrolase (target EFI-505188) from Burkhoderia ambifaria, with bound Zn

• PDB DOI: https://doi.org/10.2210/pdb4GXW/pdb

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


• Deposited: 2012-09-04 Released: 2012-09-12 
• Deposition Author(s): Vetting, M.W., Goble, A.M., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Raushel, F.M., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.181 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a cog1816 amidohydrolase (target EFI-505188) from Burkhoderia ambifaria, with bound Zn

Vetting, M.W., Goble, A.M., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Raushel, F.M., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 85.6 kDa 
• Atom Count: 7,233 
• Modeled Residue Count: 733 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase	A, B	380	Burkholderia ambifaria AMMD	Mutation(s): 0  Gene Names: Bamb_4621 EC: 3.5.4.4
UniProt
Find proteins for Q0B6Q2 (Burkholderia ambifaria (strain ATCC BAA-244 / DSM 16087 / CCUG 44356 / LMG 19182 / AMMD)) Explore Q0B6Q2  Go to UniProtKB:  Q0B6Q2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth B], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.181 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.058	α = 90
b = 66.223	β = 93.64
c = 75.432	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Vetting, M.W., Goble, A.M., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Raushel, F.M., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description