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

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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

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BR	C [auth A], D [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Smith, C.A., Buchko, G.W., Wu, R., Cort, J.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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