6MU9 | pdb_00006mu9

Beta-lactamase penicillinase from Bacillus megaterium

• PDB DOI: https://doi.org/10.2210/pdb6MU9/pdb

• Classification: LIGASE
• Organism(s): Priestia megaterium DSM 319
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-22 Released: 2018-11-07 
• Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 
  0.111 (Depositor), 0.122 (DCC) 
• R-Value Work: 
  0.101 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.102 (Depositor) 

Starting Model: experimental

Literature

Beta-lactamase penicillinase from Bacillus megaterium

Osipiuk, J., Tesar, C., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 30.8 kDa 
• Atom Count: 2,635 
• Modeled Residue Count: 263 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	276	Priestia megaterium DSM 319	Mutation(s): 0  Gene Names: penP, BMD_3363 EC: 3.5.2.6
UniProt
Find proteins for D5DH82 (Priestia megaterium (strain DSM 319 / IMG 1521)) Explore D5DH82  Go to UniProtKB:  D5DH82

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free:  0.111 (Depositor), 0.122 (DCC) 
• R-Value Work:  0.101 (Depositor), 0.110 (DCC) 
• R-Value Observed: 0.102 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36mu9

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.307	α = 97.73
b = 42.094	β = 105.52
c = 48.542	γ = 113.34

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-07 
Deposition Author(s): Osipiuk, J., Tesar, C., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2018-11-07
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description