9DZS | pdb_00009dzs

Acanthamoeba Polyphaga Mimivirus R699

• PDB DOI: https://doi.org/10.2210/pdb9DZS/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Acanthamoeba polyphaga mimivirus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-17 Released: 2025-06-11 
• Deposition Author(s): Richards, S.J., Buhlheller, C., Kim, J.S., Chen, T., Wu, J., Guo, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.195 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.179 (DCC) 

Starting Model: experimental

Literature

Acanthamoeba Polyphaga Mimivirus R699

Richards, S.J., Buhlheller, C., Kim, J.S., Chen, T., Wu, J., Guo, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.96 kDa 
• Atom Count: 3,967 
• Modeled Residue Count: 439 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
R699	A	458	Acanthamoeba polyphaga mimivirus	Mutation(s): 0  Gene Names: MIMI_R699
UniProt
Find proteins for Q5UNV6 (Acanthamoeba polyphaga mimivirus) Explore Q5UNV6  Go to UniProtKB:  Q5UNV6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	B [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
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: 1.75 Å
• R-Value Free:  0.195 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.179 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.041	α = 90
b = 71.481	β = 123.178
c = 72.626	γ = 90

Software Package:

Software Name	Purpose
DIALS	data collection
xia2	data reduction
Aimless	data scaling
PHENIX	phasing
PHASER	phasing
Coot	model building
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Richards, S.J., Buhlheller, C., Kim, J.S., Chen, T., Wu, J., Guo, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R00CA225633
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R37CA278989

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release