7VG8 | pdb_00007vg8

TYLCV Rep-DNA

• PDB DOI: https://doi.org/10.2210/pdb7VG8/pdb
• NAKB: 7VG8

• Classification: VIRAL PROTEIN
• Organism(s): Tomato yellow leaf curl virus, Tomato yellow leaf curl virus-IL [MX: SLP:11]
• Expression System: prokaryote coculture, DNA satellites
• Mutation(s): Yes 


• Deposited: 2021-09-14 Released: 2022-09-21 
• Deposition Author(s): Zhang, S.Y., Wang, C.N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.267 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

structure of TYLCV Rep complexed with ssDNA

Zhang, S.Y., Wang, C.N.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.86 kDa 
• Atom Count: 1,210 
• Modeled Residue Count: 117 
• Deposited Residue Count: 121 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication-associated protein	A	112	Tomato yellow leaf curl virus	Mutation(s): 1  Gene Names: AC1 EC: 3.1.21
UniProt
Find proteins for H6WA92 (Tomato yellow leaf curl virus) Explore H6WA92  Go to UniProtKB:  H6WA92

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-((DT)P*(DA)P*(DA)P*(DT)P*(DA)P*(DT)P*(DT)P*(DA)*(DC)P*)-3')	B [auth C]	9	Tomato yellow leaf curl virus-IL [MX: SLP:11]

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.267 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.976	α = 90
b = 67.976	β = 90
c = 40.433	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Zhang, S.Y., Wang, C.N.

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Funding Organization	Location	Grant Number
Not funded	China	--

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description