4IEG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1002/prot.24297
  • Primary Citation of Related Structures:  
    4GZK, 4IEG

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-dependent RNA polymerase P2
A, B, C, D
659Pseudomonas phage phi12Mutation(s): 1 
Gene Names: P2
UniProt
Find proteins for Q94M06 (Pseudomonas phage phi12)
Explore Q94M06 
Go to UniProtKB:  Q94M06
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94M06
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.874α = 75.16
b = 94.47β = 63.11
c = 96.481γ = 83.79
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description