9MS7 | pdb_00009ms7

Crystal structure of a putative phage endolysin identified from a metagenomic survey of Prosser, Washington soil (PWe2)

PDB DOI: https://doi.org/10.2210/pdb9MS7/pdb

Classification: HYDROLASE
Organism(s): metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-09 Released: 2025-05-21
Deposition Author(s): Smith, C.A., Buchko, G.W., Wu, R., Cort, J.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.192 (Depositor), 0.192 (DCC)
R-Value Work:
0.151 (Depositor), 0.151 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structures of two phage endolysins identified from a metagenomic survey of south-central Washington soil

Buchko, G.W., Smith, C.A., Wu, R., Alfaro, T.D., McClure, R.S., Cort, J.R., Hofmockel, K.F.

To be published.

Macromolecule Content

Total Structure Weight: 41.87 kDa
Atom Count: 3,151
Modeled Residue Count: 360
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PWe2 endolysin	A, B	182	metagenome	Mutation(s): 0
UniProt
Find proteins for A0A562R7W5 (Pseudoduganella lurida) Explore A0A562R7W5 Go to UniProtKB: A0A562R7W5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A562R7W5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	E [auth A], F [auth A], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	C [auth A], D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B]