3GKR

Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-hexapeptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Weissella viridescens FemX with the UDP-MurNAc-hexapeptide product of the alanine transfer reaction

Delfosse, V.Piton, J.Villet, R.Lecerf, M.Arthur, M.Mayer, C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FemX
A
336Weissella viridescensGene Names: femX
EC: 2.3.2.10
Find proteins for Q9EY50 (Weissella viridescens)
Go to UniProtKB:  Q9EY50
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UDP-MurNAc-peptide
B
5N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ALA
Query on ALA

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Download CCD File 
B
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
FGA
Query on FGA
B
D-gamma-peptide, C-delta linkingC5 H9 N O4

--

DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

--

UMA
Query on UMA
B
L-PEPTIDE LINKINGC23 H36 N4 O20 P2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.324α = 90.00
b = 101.836β = 102.85
c = 46.847γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
REFMACrefinement
MAR345dtbdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Database references, Derived calculations, Non-polymer description, Version format compliance
  • Version 1.2: 2012-08-01
    Type: Structure summary
  • Version 1.3: 2012-09-05
    Type: Derived calculations