3VQV

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AMPPNP (re-refined)

Structural Biology Knowledgebase: 3VQV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.187

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VQV

Classification: LIGASE

Total Structure Weight: 33899.21

Macromolecule Entities
Molecule Chains Length Organism Details
Pyrrolysine--tRNA ligase A 291 Methanosarcina mazei EC#: 6.1.1.26 IUBMB
Gene Name(s): pylS MM_1445

Small Molecules
Ligands 2 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
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: 0.219
  • R-Value Work: 0.187
  • Space Group: P 64
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.88 α = 90.00
b = 104.88 β = 90.00
c = 70.43 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-01
  • Released Date: 2013-01-02
  • Deposition author(s): Yanagisawa, T., Sumida, T., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
  • Previous versions: 2ZCD

Revision History

  • 2013-09-04
    Type: Citation | Details: Citation update