5E2F

Crystal Structure of Beta-lactamase class D from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamase YbxIA, B270Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: ybxIybdSBSU02090
EC: 3.5.2.6
UniProt
Find proteins for P54427 (Bacillus subtilis (strain 168))
Explore P54427 
Go to UniProtKB:  P54427
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54427
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
A, B L-PEPTIDE LINKINGC8 H16 N2 O3LYS
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.699α = 90
b = 68.856β = 90
c = 153.979γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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