3SD9 | pdb_00003sd9

Crystal structure of serratia fonticola SFH-I: Source of the nucleophile in the catalytic mechanism of mono-zinc metallo-beta-lactamases

• PDB DOI: https://doi.org/10.2210/pdb3SD9/pdb

• Classification: HYDROLASE
• Organism(s): Serratia fonticola
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-08 Released: 2011-07-13 
• Deposition Author(s): Fonseca, F., Saavedra, M.J., Correia, A., Spencer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Serratia fonticola Sfh-I: Activation of the Nucleophile in Mono-Zinc Metallo-beta-Lactamases

Fonseca, F., Bromley, E.H.C., Saavedra, M.J., Correia, A., Spencer, J.

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: 52.72 kDa 
• Atom Count: 3,930 
• Modeled Residue Count: 459 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	233	Serratia fonticola	Mutation(s): 0  Gene Names: blaSfh-I, sfhI EC: 3.5.2.6
UniProt
Find proteins for Q9RMI1 (Serratia fonticola) Explore Q9RMI1  Go to UniProtKB:  Q9RMI1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.965	α = 90
b = 86.412	β = 90.07
c = 72.193	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Fonseca, F., Saavedra, M.J., Correia, A., Spencer, J.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description