4RU3 | pdb_00004ru3

Crystal structure of the cell puncturing protein Orf41 from Pseudomonas phage SN

• PDB DOI: https://doi.org/10.2210/pdb4RU3/pdb

• Classification: CELL INVASION
• Organism(s): Pseudomonas phage SN
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-18 Released: 2015-11-18 
• Deposition Author(s): Browning, C., Shneider, M.M., Leiman, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 
  0.150 (Depositor), 0.151 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Literature

Crystal structure of the cell puncturing protein Orf41 from Pseudomonas phage SN

Browning, C., Shneider, M.M., Leiman, P.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 24.27 kDa 
• Atom Count: 2,065 
• Modeled Residue Count: 205 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
puncturing protein gp41	A	221	Pseudomonas phage SN	Mutation(s): 0  Gene Names: ORF41
UniProt
Find proteins for B7VFI6 (Pseudomonas phage SN) Explore B7VFI6  Go to UniProtKB:  B7VFI6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free:  0.150 (Depositor), 0.151 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.54	α = 90
b = 84.54	β = 90
c = 84.54	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Browning, C., Shneider, M.M., Leiman, P.G.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Advisory, Refinement description
• Version 1.2: 2019-09-25
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2024-02-28
  Changes: Advisory, Data collection, Database references, Derived calculations