6E1R | pdb_00006e1r

Crystal structure of the Acinetobacter phage vB_ApiP_P1 tailspike protein

• PDB DOI: https://doi.org/10.2210/pdb6E1R/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter phage vB_ApiP_P1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-10 Released: 2019-07-17 
• Deposition Author(s): Plattner, M., Shneider, M.M., Oliveira, H., Azeredo, J., Leiman, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of the Acinetobacter phage vB_ApiP_P1 tailspike protein

Plattner, M., Shneider, M.M., Oliveira, H., Azeredo, J., 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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 356.63 kDa 
• Atom Count: 25,193 
• Modeled Residue Count: 3,263 
• Deposited Residue Count: 3,324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tailspike protein	A, B, C, D, E, F	554	Acinetobacter phage vB_ApiP_P1	Mutation(s): 0  Gene Names: P1_43
UniProt
Find proteins for A0A221SBY4 (Acinetobacter phage vB_ApiP_P1) Explore A0A221SBY4  Go to UniProtKB:  A0A221SBY4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	G [auth A], J [auth C], L [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth B], I [auth C], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.123	α = 90
b = 90.015	β = 90
c = 508.604	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
HKL2Map	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-17 
Deposition Author(s): Plattner, M., Shneider, M.M., Oliveira, H., Azeredo, J., Leiman, P.G.

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary