1VFG

Crystal structure of tRNA nucleotidyltransferase complexed with a primer tRNA and an incoming ATP analog

Structural Biology Knowledgebase: 1VFG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.230

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1VFG

Classification: TRANSFERASE / RNA

Total Structure Weight: 140766.05


Macromolecule Entities
Molecule Chains Length Organism Details
poly A polymerase A, B 390 Aquifex aeolicus EC#: 2.7.7.19 IUBMB
Fragment: residues 1-390
Gene Name(s): pcnB1 aq_411
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (75-MER) C, D 75 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
APC
Query on APC

A, B DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE (Synonym)
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287
  • R-Value Work: 0.230
  • Space Group: P 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 109.48 α = 90.00
b = 125.90 β = 90.00
c = 58.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-04-13
  • Released Date: 2004-08-10
  • Deposition author(s): Tomita, K., Fukai, S., Ishitani, R., Ueda, T., Takeuchi, N., Vassylyev, D.G., Nureki, O., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4