5GNF

Crystal structure of anti-CRISPR protein AcrF3

• PDB DOI: https://doi.org/10.2210/pdb5GNF/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pseudomonas phage JBD5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-20 Released: 2016-09-21 
• Deposition Author(s): Wang, J., Wang, Y.
• Funding Organization(s): National Natural Science Foundation of China, Ministry of Science and Technology (China), Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR/Cas responses

Wang, J., Ma, J., Cheng, Z., Meng, X., You, L., Wang, M., Zhang, X., Wang, Y.

(2016) Cell Res 26: 1165-1168

• PubMed: 27585537 
• DOI: https://doi.org/10.1038/cr.2016.103
• Primary Citation of Related Structures:  
  5GNF, 5GQH

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Organizational Affiliation: 

Key Laboratory of RNA Biology, Beijing 100101, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 31.91 kDa 
• Atom Count: 2,503 
• Modelled Residue Count: 272 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein AcrF3	A, B	140	Pseudomonas phage JBD5	Mutation(s): 0  Gene Names: JBD5_035
UniProt
Find proteins for L7P7R7 (Pseudomonas phage JBD5) Explore L7P7R7  Go to UniProtKB:  L7P7R7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.944	α = 90
b = 84.944	β = 90
c = 63.155	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Wang, J., Wang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91440201
Ministry of Science and Technology (China)	China	2014CB910102
Chinese Academy of Sciences	China	XDB08010203

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2017-10-18
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations