4EWF | pdb_00004ewf

The crystal structure of beta-lactamase from Sphaerobacter thermophilus DSM 20745

• PDB DOI: https://doi.org/10.2210/pdb4EWF/pdb

• Classification: HYDROLASE
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-04-26 Released: 2012-09-19 
• Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.209 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

The crystal structure of beta-lactamase from Sphaerobacter thermophilus DSM 20745

Wu, R., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.9 kDa 
• Atom Count: 8,292 
• Modeled Residue Count: 1,059 
• Deposited Residue Count: 1,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	275	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  Gene Names: Sthe_2032 EC: 3.5.2.6
UniProt
Find proteins for D1C5R0 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C5R0  Go to UniProtKB:  D1C5R0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth B], H [auth C], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	I [auth C]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.209 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34EWF

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.5	α = 90
b = 215.551	β = 90
c = 83.816	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MLPHARE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary