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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.193 (Depositor), 0.201 (DCC)
R-Value Work:
0.168 (Depositor), 0.177 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Structure of Klebsiella Phage P560 depolymerase

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

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7S6TZU4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth B] G [auth B] H [auth B] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.193 (Depositor), 0.201 (DCC)
R-Value Work: 0.168 (Depositor), 0.177 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.