9CRZ | pdb_00009crz

Acanthamoeba Polyphaga Mimivirus R655

• PDB DOI: https://doi.org/10.2210/pdb9CRZ/pdb

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


• Deposited: 2024-07-23 Released: 2025-08-06 
• Deposition Author(s): Morin, K.H., Buhlheller, C., Kim, J.S., Richards, S.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: 2.10 Å
• R-Value Free: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.212 (DCC) 

Starting Model: in silico

Literature

Acanthamoeba Polyphaga Mimivirus R655

Kim, J.S., Buhlheller, C., Morin, K.H., Gilliam, M.E., Zhang, B., Richards, S.J., Miller, T.M., Guo, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 80.68 kDa 
• Atom Count: 5,647 
• Modeled Residue Count: 624 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glycosyltransferase R655	A, B	346	Acanthamoeba polyphaga mimivirus	Mutation(s): 0  Gene Names: MIMI_R655 EC: 2
UniProt
Find proteins for Q5UQ62 (Acanthamoeba polyphaga mimivirus) Explore Q5UQ62  Go to UniProtKB:  Q5UQ62

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	C [auth A], E [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MN (Subject of Investigation/LOI)	D [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.212 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.634	α = 90
b = 96.213	β = 90
c = 133.454	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: 2025-08-06 
Deposition Author(s): Morin, K.H., Buhlheller, C., Kim, J.S., Richards, S.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: 2025-08-06
  Type: Initial release