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- PDB-7bio: Crystal structure of monooxygenase RslO4 from Streptomyces bottro... -

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Basic information

Entry
Database: PDB / ID: 7bio
TitleCrystal structure of monooxygenase RslO4 from Streptomyces bottropensis
ComponentsMonooxygenase/putative anthronoxygenase
KeywordsOXIDOREDUCTASE / Rishirilides biosynthesis
Function / homologyABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Dimeric alpha-beta barrel / monooxygenase activity / ACETATE ION / ETHANOL / PHOSPHATE ION / Monooxygenase/putative anthronoxygenase
Function and homology information
Biological speciesStreptomyces bottropensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 Å
AuthorsZhang, L. / Zuo, C. / Alali, A. / Bechthold, A. / Einsle, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG1976 Germany
CitationJournal: Mol Biotechnol. / Year: 2021
Title: Biosynthesis of the Tricyclic Aromatic Type II Polyketide Rishirilide: New Potential Third Ring Oxygenation after Three Cyclization Steps.
Authors: Alali, A. / Zhang, L. / Li, J. / Zuo, C. / Wassouf, D. / Yan, X. / Schwarzer, P. / Gunther, S. / Einsle, O. / Bechthold, A.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monooxygenase/putative anthronoxygenase
B: Monooxygenase/putative anthronoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,77210
Polymers26,3162
Non-polymers4568
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-17 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.681, 83.681, 82.346
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Monooxygenase/putative anthronoxygenase


Mass: 13157.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces bottropensis (bacteria) / Gene: rslO4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: W8QLE0
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6% ethanol, 0.1 M ammonium acetate (pH 5.5) and 1.5 M phosphate (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.795→72.47 Å / Num. obs: 25998 / % possible obs: 94.4 % / Redundancy: 19.7 % / CC1/2: 1 / Net I/σ(I): 25.7
Reflection shellResolution: 1.795→1.912 Å / Num. unique obs: 1300 / CC1/2: 0.638

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KNG

3kng


Resolution: 1.795→41.84 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 2412 4.86 %
Rwork0.1828 47219 -
obs0.1839 25998 82.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.14 Å2 / Biso mean: 50.1784 Å2 / Biso min: 30.39 Å2
Refinement stepCycle: final / Resolution: 1.795→41.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 62 148 1968
Biso mean--61.86 52.74 -
Num. residues----217
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8316-1.87140.4187380.337282124
1.8714-1.91490.34891060.297157148
1.9149-1.96280.27791000.2747198459
1.9628-2.01590.28711420.279257677
2.0752-2.14220.26981560.2461327697
2.1422-2.21880.30621610.23453363100
2.2188-2.30760.25241700.23083396100
2.3076-2.41260.23831960.20813326100
2.4126-2.53980.25381380.20373406100
2.5398-2.69890.27221540.21523393100
2.6989-2.90720.23751960.21783338100
2.9072-3.19970.20981890.20533360100
3.1997-3.66240.19971580.17623390100
3.6624-4.61340.16041490.13623411100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0471.3167-0.02433.4062-1.02831.71360.053-0.14020.31770.33990.09960.2123-0.40790.0033-0.12370.3835-0.0581-0.0040.26960.01580.3052-28.749235.92576.4527
21.294-1.20250.50793.0109-0.96462.6648-0.1013-0.0066-0.13420.1395-0.02140.04190.18470.05610.09930.3037-0.1137-0.0150.25690.00150.2844-27.291523.13446.2228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 2:107)A2 - 107
2X-RAY DIFFRACTION2(chain B and resseq 2:112)B2 - 112

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