4IEG

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

• PDB DOI: https://doi.org/10.2210/pdb4IEG/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas phage phi12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-12-13 Released: 2013-07-24 
• Deposition Author(s): Ren, Z., Franklin, M.C., Ghose, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.278 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

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

Ren, Z., C Franklin, M., Ghose, R.

(2013) Proteins 81: 1479-1484

• PubMed: 23568335 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 301.94 kDa 
• Atom Count: 22,601 
• Modelled Residue Count: 2,576 
• Deposited Residue Count: 2,636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-dependent RNA polymerase P2	A, B, C, D	659	Pseudomonas phage phi12	Mutation(s): 1  Gene Names: P2 EC: 2.7.7.48
UniProt
Find proteins for Q94M06 (Pseudomonas phage phi12) Explore Q94M06  Go to UniProtKB:  Q94M06

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.278 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.874	α = 75.16
b = 94.47	β = 63.11
c = 96.481	γ = 83.79

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Ren, Z., Franklin, M.C., Ghose, R.

Revision History  

• 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