9MS6 | pdb_00009ms6

Crystal structure of a putative phage endolysin identified from a metagenomic survey of Prosser, Washington soil (PWe1)

PDB DOI: https://doi.org/10.2210/pdb9MS6/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: 2.15 Å
R-Value Free:
0.272 (Depositor), 0.274 (DCC)
R-Value Work:
0.212 (Depositor), 0.214 (DCC)
R-Value Observed:
0.215 (Depositor)

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

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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: 23.98 kDa
Atom Count: 1,521
Modeled Residue Count: 188
Deposited Residue Count: 210
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PWe1 endolysin	A	210	metagenome	Mutation(s): 0
UniProt
Find proteins for A0A8D5AJ83 (Methylogaea oryzae) Explore A0A8D5AJ83 Go to UniProtKB: A0A8D5AJ83
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D5AJ83
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.272 (Depositor), 0.274 (DCC)
R-Value Work: 0.212 (Depositor), 0.214 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.842	α = 90
b = 64.842	β = 90
c = 85.573	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release

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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.