8R2B | pdb_00008r2b

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

PDB DOI: https://doi.org/10.2210/pdb8R2B/pdb

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

Deposited: 2023-11-03 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: 1.80 Å
R-Value Free:
0.230 (Depositor), 0.239 (DCC)
R-Value Work:
0.192 (Depositor), 0.201 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8R2B

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: 34.4 kDa
Atom Count: 2,423
Modeled Residue Count: 261
Deposited Residue Count: 296
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RN64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XN0 (Subject of Investigation/LOI) Query on XN0 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-nogalamycinone C₂₉ H₃₂ O₁₂ XDICDWFRDRDUMQ-GUXZDVRLSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.230 (Depositor), 0.239 (DCC)
R-Value Work: 0.192 (Depositor), 0.201 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.628	α = 90
b = 62.281	β = 90
c = 89.814	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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

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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.