4II9

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

Structural Biology Knowledgebase: 4II9 SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4II9

Classification: TRANSFERASE / PEPTIDE / RNA

Total Structure Weight: 41440.07


Macromolecule Entities
Molecule Chains Length Organism Details
FemX A 343 Weissella viridescens EC#: 2.3.2.10 IUBMB
Gene Name(s): femX
5-mer peptide B 5 synthetic
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (5'-R(P*CP*CP*(A9Z))-3') C 3 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UDP
Query on UDP

B URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MUB
Query on MUB

B N-ACETYLMURAMIC ACID
C11 H19 N O8
MNLRQHMNZILYPY-MDMHTWEWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
FGA
Query on FGA
B D-gamma-peptide, C-delta linking C5 H9 N O4 --
DAL
Query on DAL
B D-PEPTIDE LINKING C3 H7 N O2 --
A9Z
Query on A9Z
C RNA LINKING C14 H19 N8 O6 P A

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
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.13 α = 90.00
b = 101.77 β = 102.60
c = 46.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-20
  • Released Date: 2013-07-03
  • Deposition author(s): Li de la Sierra-Gallay, I., Fonvielle, M., van Tilbeurgh, H., Arthur, M., Etheve-Quelquejeu, M.

Revision History

  • 2013-08-07
    Type: Citation | Details: Citation update