8R2E | pdb_00008r2e

X-ray crystallographic structure of SnoaL2 in complex with the polyketide reaction product

PDB DOI: https://doi.org/10.2210/pdb8R2E/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces nogalater
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-04 Released: 2024-08-07
Deposition Author(s): Schnell, R., Schneider, G.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.238 (Depositor), 0.250 (DCC)
R-Value Work:
0.195 (Depositor), 0.200 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mechanism of Two-Component Mono-Oxygenases Involved in Anthracycline 1-Hydroxylation

Wandi, B.N., Dinis, P., Siitonen, V., Schneider, G., Schnell, R., Metsa-Ketele, M.

(2024) ACS Catal

DOI: https://doi.org/10.1021/acscatal.4c02623

Macromolecule Content

Total Structure Weight: 34.41 kDa
Atom Count: 2,310
Modeled Residue Count: 257
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SnoL	A, B	148	Streptomyces nogalater	Mutation(s): 0 Gene Names: snoL
UniProt
Find proteins for Q9RN64 (Streptomyces nogalater) Explore Q9RN64 Go to UniProtKB: Q9RN64
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RN64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XN8 (Subject of Investigation/LOI) Query on XN8 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3',4'-demethoxy-nogalose-1-hydroxy-nogalamycinone C₂₉ H₃₂ O₁₃ JMZPXXMAMHNKHM-WOAFMFBISA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.238 (Depositor), 0.250 (DCC)
R-Value Work: 0.195 (Depositor), 0.200 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.96	α = 90
b = 62.195	β = 90
c = 89.644	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2018-03999

Revision History (Full details and data files)

Version 1.0: 2024-08-07
Type: Initial release

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.