4DLF

Crystal structure of an amidohydrolase (COG3618) from burkholderia multivorans (TARGET EFI-500235) with bound ZN, space group P3221

• PDB DOI: https://doi.org/10.2210/pdb4DLF/pdb

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


• Deposited: 2012-02-06 Released: 2012-02-29 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Seidel, R.D., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Al Obaidi, N.F., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.228 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an amidohydrolase (COG3618) from burkholderia multivorans (target efi-500235) with bound ZN, space group P3221

Vetting, M.W., Toro, R., Bhosle, R., Seidel, R.D., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Al Obaidi, N.F., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., 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)

Macromolecule Content

• Total Structure Weight: 34.31 kDa 
• Atom Count: 2,546 
• Modelled Residue Count: 287 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase 2	A	303	Burkholderia multivorans ATCC 17616	Mutation(s): 0  Gene Names: Bmul_3602, BMULJ_04915 EC: 3.1.1.120
UniProt
Find proteins for A0A0H3KNC4 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KNC4  Go to UniProtKB:  A0A0H3KNC4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	G [auth A], H [auth A], I [auth A], J [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.228 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.3	α = 90
b = 75.3	β = 90
c = 142.45	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Seidel, R.D., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Al Obaidi, N.F., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description