6H8O | pdb_00006h8o

Crystal structure of the Master-Rep protein nuclease domain from the Faba Bean Necrotic Yellows Virus

• PDB DOI: https://doi.org/10.2210/pdb6H8O/pdb

• Classification: REPLICATION
• Organism(s): Faba bean necrotic yellows virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-02 Released: 2018-08-22 
• Deposition Author(s): Moncalian, G., Gonzalez-Montes, L.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Starting Model: other

Literature

Crystal structure of the Master-Rep protein nuclease domain from the Faba Bean Necrotic Yellows Virus

Moncalian, G., Gonzalez-Montes, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.68 kDa 
• Atom Count: 1,864 
• Modeled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication-associated protein	A, B	95	Faba bean necrotic yellows virus	Mutation(s): 0  EC: 3.6.1 (UniProt), 3.1.21 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for O39828 (Faba bean necrotic yellows virus (isolate Syrian SV292-88)) Explore O39828  Go to UniProtKB:  O39828

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.23	α = 90
b = 94.23	β = 90
c = 45.61	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-22 
Deposition Author(s): Moncalian, G., Gonzalez-Montes, L.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2014-55534-C2-2-P

Revision History  

• Version 1.0: 2018-08-22
  Type: Initial release
  
• Version 2.0: 2018-10-03
  Changes: Atomic model, Data collection, Derived calculations, Refinement description
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description