5ZQA

Crystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the apo form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal Structures of Penicillin-Binding Protein D2 from Listeria monocytogenes and Structural Basis for Antibiotic Specificity

Jeong, J.H., Cha, H.J., Kim, Y.G.

(2018) Antimicrob. Agents Chemother. 62: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lmo2812 protein
A
276Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)Mutation(s): 0 
Find proteins for Q8Y3M3 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Go to UniProtKB:  Q8Y3M3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG
Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.669α = 90.00
b = 74.582β = 90.00
c = 74.955γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-04-18 
  • Released Date: 2018-07-25 
  • Deposition Author(s): Jeong, J.H., Kim, Y.G.
Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of--

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-22
    Type: Data collection, Database references
  • Version 1.2: 2018-09-12
    Type: Data collection, Database references