5E2F | pdb_00005e2f

Crystal Structure of Beta-lactamase class D from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb5E2F/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-10-01 Released: 2015-10-14 
• Deposition Author(s): Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., MCSG, Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.152 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Literature

Crystal Structure of Beta-lactamase class D from Bacillus subtilis

Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.06 kDa 
• Atom Count: 4,702 
• Modeled Residue Count: 474 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase YbxI	A, B	270	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: ybxI, ybdS, BSU02090 EC: 3.5.2.6
UniProt
Find proteins for P54427 (Bacillus subtilis (strain 168)) Explore P54427  Go to UniProtKB:  P54427

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A], D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A, B	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.152 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.699	α = 90
b = 68.856	β = 90
c = 153.979	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., MCSG, Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2022-03-30
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary