4II9

Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure of FemXWv in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA(Ala) to Peptidoglycan Precursors

Fonvielle, M.Li de La Sierra-Gallay, I.El-Sagheer, A.H.Lecerf, M.Patin, D.Mellal, D.Mayer, C.Blanot, D.Gale, N.Brown, T.van Tilbeurgh, H.Etheve-Quelquejeu, M.Arthur, M.

(2013) Angew.Chem.Int.Ed.Engl. 52: 7278-7281


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FemX
A
343Weissella viridescensGene Names: femX
EC: 2.3.2.10
Find proteins for Q9EY50 (Weissella viridescens)
Go to UniProtKB:  Q9EY50
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5-mer peptide
B
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*CP*(A9Z))-3')C3N/A
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
MUB
Query on MUB

Download SDF File 
Download CCD File 
B
N-ACETYLMURAMIC ACID
C11 H19 N O8
MNLRQHMNZILYPY-MDMHTWEWSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
B
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-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

--

A9Z
Query on A9Z
C
RNA LINKINGC14 H19 N8 O6 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.130α = 90.00
b = 101.770β = 102.60
c = 46.320γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
MXdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references