7VUL | pdb_00007vul

Structure of Klebsiella Phage P560 depolymerase

• PDB DOI: https://doi.org/10.2210/pdb7VUL/pdb

• Classification: LYASE
• Organism(s): Klebsiella phage P560
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-11-02 Released: 2022-11-16 
• Deposition Author(s): Li, M., Chen, R., Zhang, S., Zhang, W.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Structure of Klebsiella Phage P560 depolymerase

Li, M., Chen, R., Zhang, S., Zhang, W.

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: 211.58 kDa 
• Atom Count: 15,195 
• Modeled Residue Count: 1,876 
• Deposited Residue Count: 1,989 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-contractile tail fiber protein	A, B, C	663	Klebsiella phage P560	Mutation(s): 0
UniProt
Find proteins for A0A7S6TZU4 (Klebsiella phage P560) Explore A0A7S6TZU4  Go to UniProtKB:  A0A7S6TZU4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth C], J [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.665	α = 90
b = 126.842	β = 90
c = 144.993	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Li, M., Chen, R., Zhang, S., Zhang, W.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection