2V6I

Kokobera Virus Helicase

• PDB DOI: https://doi.org/10.2210/pdb2V6I/pdb

• Classification: HYDROLASE
• Organism(s): Kokobera virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-07-18 Released: 2008-03-25 
• Deposition Author(s): Speroni, S., De Colibus, L., Coutard, B., Canard, B., Mattevi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.275 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Structure and Biochemical Analysis of Kokobera Virus Helicase

Speroni, S., De Colibus, L., Mastrangelo, E., Gould, E., Coutard, B., Forrester, N.L., Blanc, S., Canard, B., Mattevi, A.

(2008) Proteins 70: 1120

• PubMed: 18004778 
• DOI: https://doi.org/10.1002/prot.21812
• Primary Citation of Related Structures:  
  2V6I, 2V6J

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Organizational Affiliation: 

Department of Genetics and Microbiology, University of Pavia, via Ferrata 1, Pavia 27100 Italy.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 49.18 kDa 
• Atom Count: 3,550 
• Modelled Residue Count: 421 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA HELICASE	A	431	Kokobera virus	Mutation(s): 0
UniProt
Find proteins for Q32ZD5 (Kokobera virus) Explore Q32ZD5  Go to UniProtKB:  Q32ZD5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP	B [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.275 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.269	α = 90
b = 88.269	β = 90
c = 139.087	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Speroni, S., De Colibus, L., Coutard, B., Canard, B., Mattevi, A.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description