7RJJ

Crystal Structure of the Peptidoglycan Binding Domain of the Outer Membrane Protein (OmpA) from Klebsiella pneumoniae with bound D-alanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal Structure of the Peptidoglycan Binding Domain of the Outer Membrane Protein (OmpA) from Klebsiella pneumoniae with bound D-alanine.

Minasov, G.Shuvalova, L.Kiryukhina, O.Dubrovska, I.Satchell, K.J.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OmpA family proteinA, B127Klebsiella pneumoniae subsp. pneumoniaeMutation(s): 0 
Gene Names: C4Z38_016670EJ893_12145I5002_15200JMY88_11465
UniProt
Find proteins for A0A422WJQ0 (Klebsiella pneumoniae subsp. pneumoniae)
Explore A0A422WJQ0 
Go to UniProtKB:  A0A422WJQ0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAL (Subject of Investigation/LOI)
Query on DAL

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.887α = 90
b = 41.887β = 90
c = 267.934γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release