5E2F

Crystal Structure of Beta-lactamase class D from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase YbxI
A, B
270Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ybxI (ybdS)
EC: 3.5.2.6
Find proteins for P54427 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P54427
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
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: 1.3 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.699α = 90.00
b = 68.856β = 90.00
c = 153.979γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data reduction
PHENIXrefinement
SBC-Collectdata collection
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release