6C72 | pdb_00006c72

Crystal structure of a tailspike protein gp49 from Acinetobacter baumannii bacteriophage Fri1, a capsular polysaccharide depolymerase

• PDB DOI: https://doi.org/10.2210/pdb6C72/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter phage Fri1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-19 Released: 2019-01-23 
• Deposition Author(s): Buth, S.A., Garcon, A., Popova, A.V., Shneider, M.M., Leiman, P.G.
• Funding Organization(s): SNF

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: other

Literature

Exopolysaccharide degrading enzymes - specificity determinants of Acinetobacter baumannii phages

Buth, S.A., Shneider, M.M., Popova, A.V., Shashkov, A.S., Senchenkova, S.N., Knirel, Y., 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

Macromolecule Content 

• Total Structure Weight: 198.16 kDa 
• Atom Count: 15,043 
• Modeled Residue Count: 1,737 
• Deposited Residue Count: 1,791 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Particle-associated glycoside hydrolase	A, B, C	597	Acinetobacter phage Fri1	Mutation(s): 0  Gene Names: Fri1_49
UniProt
Find proteins for A0A0H4TJ34 (Acinetobacter phage Fri1) Explore A0A0H4TJ34  Go to UniProtKB:  A0A0H4TJ34

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	AA [auth B], BA [auth B], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.462	α = 90
b = 98.664	β = 91.81
c = 148.704	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Buth, S.A., Garcon, A., Popova, A.V., Shneider, M.M., Leiman, P.G.

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Funding Organization	Location	Grant Number
SNF	Switzerland	310030_144243

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-04-03
  Changes: Refinement description