6W2Z | pdb_00006w2z

Crystal Structure of the Beta Lactamase Class A PenP from Bacillus subtilis in the Complex with the Non-beta- lactam Beta-lactamase Inhibitor Avibactam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.

Inniss, N.L.Minasov, G.Chang, C.Tan, K.Kim, Y.Maltseva, N.Stogios, P.Filippova, E.Michalska, K.Osipiuk, J.Jaroszewki, L.Godzik, A.Savchenko, A.Joachimiak, A.Anderson, W.F.Satchell, K.J.F.

(2025) Microbiol Resour Announc : e0020025-e0020025

  • DOI: https://doi.org/10.1128/mra.00200-25
  • Primary Citation of Related Structures:  
    5UME, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5WP0, 6AON, 6AOO, 6AZI, 6B5F, 6B8D, 6BK7, 6BLB, 6C8Q, 6PU9, 6PUA, 6PXA, 6W2Z, 9BZN, 9BZQ, 9BZR

  • PubMed Abstract: 

    Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.


  • Organizational Affiliation
    • Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
275Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: penPBSU18800
EC: 3.5.2.6
UniProt
Find proteins for P39824 (Bacillus subtilis (strain 168))
Explore P39824 
Go to UniProtKB:  P39824
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39824
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.681α = 90
b = 85.456β = 94.969
c = 70.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary
  • Version 1.3: 2025-06-18
    Changes: Database references