7KII

Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+

• PDB DOI: https://doi.org/10.2210/pdb7KII/pdb
• NAKB: 7KII

• Classification: REPLICATION/DNA
• Organism(s): Muscovy duck circovirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-10-23 Released: 2021-11-17 
• Deposition Author(s): Tompkins, K.J., Gordon, W.R., Shi, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.184 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Literature

Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site and Mn2+

Tompkins, K.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 15.61 kDa 
• Atom Count: 1,234 
• Modelled Residue Count: 113 
• Deposited Residue Count: 121 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent helicase Rep	A	111	Muscovy duck circovirus	Mutation(s): 1
UniProt
Find proteins for D2JZX8 (Muscovy duck circovirus) Explore D2JZX8  Go to UniProtKB:  D2JZX8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')	B [auth C]	10	Muscovy duck circovirus

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.184 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.417	α = 90
b = 66.343	β = 90
c = 71.259	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Tompkins, K.J., Gordon, W.R., Shi, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM119483
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description