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- PDB-8xu7: Crystal structure of Lsd18 in complex with a product -

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Basic information

Entry
Database: PDB / ID: 8xu7
TitleCrystal structure of Lsd18 in complex with a product
ComponentsPutative epoxidase LasC
KeywordsFLAVOPROTEIN / flavin-dependent monooxygenase / epoxidation
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / antibiotic biosynthetic process / FAD binding / monooxygenase activity
Similarity search - Function
FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-LSB / Putative epoxidase LasC
Similarity search - Component
Biological speciesStreptomyces lasalocidi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDeng, Y.M. / Chen, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21807088 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Structural Basis of Sequential Enantioselective Epoxidation by a Flavin-Dependent Monooxygenase in Lasalocid A Biosynthesis.
Authors: Wang, Q. / Deng, Y. / Viera, D. / Liu, X. / Liu, N. / Hu, Y. / Hu, X. / Wei, H. / Zhou, Q. / Lan, T. / He, W. / Chen, X. / Kim, C.Y.
History
DepositionJan 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative epoxidase LasC
B: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4409
Polymers105,2932
Non-polymers3,1477
Water6,233346
1
A: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9694
Polymers52,6471
Non-polymers1,3233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4715
Polymers52,6471
Non-polymers1,8244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.037, 62.234, 76.294
Angle α, β, γ (deg.)74.79, 81.97, 76.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative epoxidase LasC / Lasalocid biosynthesis protein Lsd18


Mass: 52646.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lasalocidi (bacteria) / Gene: lsd18, lasC / Production host: Escherichia coli (E. coli)
References: UniProt: B5M9L6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-LSB / (4R,5S)-3-((2R,3S,4S)-2-ethyl-5-((2R,3R)-2-ethyl-3-(2-((2R,3R)-2-ethyl-3-methyloxiran-2-yl)ethyl)oxiran-2-yl)-3-hydroxy-4-methylpentanoyl)-4-methyl-5-phenyloxazolidin-2-one / (4R,5S)-3-[(2R,3S,4S)-2-ethyl-5-[(3R)-2-ethyl-3-[2-[(2R,3R)-2-ethyl-3-methyl-oxiran-2-yl]ethyl]oxiran-2-yl]-3-hydroxy-4-methyl-pentanoyl]-4-methyl-5-phenyl-1,3-oxazolidin-2-one


Mass: 501.655 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H43NO6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.1 M Tris pH7.5, 1.0 M NaCl, 32% (w/v) PEG8000, 4% tert-butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→19.612 Å / Num. obs: 40337 / % possible obs: 98 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.052 / Rrim(I) all: 0.136 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3490 / CC1/2: 0.332 / Rpim(I) all: 0.274 / Rrim(I) all: 0.708 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8UP4

8up4


Resolution: 2.2→19.612 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 1936 4.81 %
Rwork0.227 --
obs0.2291 40284 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6971 0 159 346 7476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037283
X-RAY DIFFRACTIONf_angle_d0.6259946
X-RAY DIFFRACTIONf_dihedral_angle_d20.7112637
X-RAY DIFFRACTIONf_chiral_restr0.0441134
X-RAY DIFFRACTIONf_plane_restr0.0051296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2550.34741780.29782687X-RAY DIFFRACTION97
2.255-2.31590.31221290.27672721X-RAY DIFFRACTION97
2.3159-2.38390.36221230.27252761X-RAY DIFFRACTION97
2.3839-2.46080.32631550.27032704X-RAY DIFFRACTION98
2.4608-2.54850.35951090.26092735X-RAY DIFFRACTION98
2.5485-2.65030.31921520.24852732X-RAY DIFFRACTION98
2.6503-2.77060.31841320.25772732X-RAY DIFFRACTION98
2.7706-2.91630.28551380.25932729X-RAY DIFFRACTION98
2.9163-3.09830.32031350.24452751X-RAY DIFFRACTION98
3.0983-3.33650.26771430.23522738X-RAY DIFFRACTION98
3.3365-3.67030.25791220.21372799X-RAY DIFFRACTION99
3.6703-4.19680.23881370.20272732X-RAY DIFFRACTION99
4.1968-5.27050.21681530.17682759X-RAY DIFFRACTION99
5.2705-19.6120.20261300.20222768X-RAY DIFFRACTION99

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