4AMQ | pdb_00004amq

A Megaviridae Orfan gene encodes a new nucleotidyl transferase

• PDB DOI: https://doi.org/10.2210/pdb4AMQ/pdb

• Classification: TRANSFERASE
• Organism(s): Acanthamoeba polyphaga mimivirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-13 Released: 2013-03-20 
• Deposition Author(s): Lartigue, A., Claverie, J.M., Priet, S., Abergel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

A Megaviridae Orphan Gene Encodes a New Nucleotidyl Transferase

Ciaccafava, A., Lartigue, A., Mansuelle, P., Jeudy, S., Abergel, C.

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)

Macromolecule Content 

• Total Structure Weight: 48.47 kDa 
• Atom Count: 2,995 
• Modeled Residue Count: 341 
• Deposited Residue Count: 407 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L544	A	407	Acanthamoeba polyphaga mimivirus	Mutation(s): 0
UniProt
Find proteins for Q5UQA5 (Acanthamoeba polyphaga mimivirus) Explore Q5UQA5  Go to UniProtKB:  Q5UQA5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.445	α = 90
b = 91.092	β = 90
c = 152.994	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Lartigue, A., Claverie, J.M., Priet, S., Abergel, C.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary