4D25

Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA and AMPPNP

Structural Biology Knowledgebase: 4D25 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4D25

Classification: HYDROLASE

Total Structure Weight: 50628.39


Macromolecule Entities
Molecule Chains Length Organism Details
BMVLG PROTEIN A 434 Bombyx mori Fragment: HELICASE, RESIDUES 135-564
Mutation: E339Q, R342C
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*UP*GP*AP*CP*AP*UP)-3' D 6 Bombyx mori

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

A PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

D GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.208
  • R-Value Work: 0.171
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 52.48 α = 90.00
b = 78.57 β = 90.00
c = 104.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-05-07
  • Released Date: 2014-06-18
  • Deposition author(s): Spinelli, P., Pillai, R.S., Kadlec, J., Cusack, S.

Revision History

  • 2014-07-02
    Type: Citation | Details: JRNL