4IEG

Structure and interactions of the RNA-dependent RNA polymerase from bacteriophage phi12 (P1 crystal form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the RNA-directed RNA Polymerase from the cystovirus 12.

Ren, Z.C Franklin, M.Ghose, R.

(2013) Proteins 81: 1479-1484

  • DOI: 10.1002/prot.24297
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have determined the structure of P2, the self-priming RdRp from cystovirus φ12 in two crystal forms (A, B) at resolutions of 1.7 Å and 2.1 Å. Form A contains Mg(2+) bound at a site that deviates from the canonical noncatalytic position seen in for ...

    We have determined the structure of P2, the self-priming RdRp from cystovirus φ12 in two crystal forms (A, B) at resolutions of 1.7 Å and 2.1 Å. Form A contains Mg(2+) bound at a site that deviates from the canonical noncatalytic position seen in form B. These structures provide insight into the temperature sensitivity of a ts-mutant. However, the tunnel through which template ssRNA accesses the active site is partially occluded by a flexible loop; this feature, along with suboptimal positioning of other structural elements that prevent the formation of a stable initiation complex, indicate an inactive conformation in crystallo.


    Organizational Affiliation

    Department of Chemistry, The City College of New York, New York, New York 10031, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-dependent RNA polymerase P2
A, B, C, D
659Pseudomonas phage phi12Mutation(s): 1 
Gene Names: 2
Find proteins for Q94M06 (Pseudomonas phage phi12)
Go to UniProtKB:  Q94M06
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.217 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 87.874α = 75.16
b = 94.470β = 63.11
c = 96.481γ = 83.79
Software Package:
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references