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- PDB-9iwv: Crystal structure of Lsd18 after incubation with the substrate -

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Basic information

Entry
Database: PDB / ID: 9iwv
TitleCrystal structure of Lsd18 after incubation with the substrate
ComponentsPutative epoxidase LasC
KeywordsFLAVOPROTEIN / a flavin-dependent monooxygenase / epoxidase
Function / homologyOxidoreductases; 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 / FAD-binding domain / FAD binding domain / antibiotic biosynthetic process / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Putative epoxidase LasC
Function and homology information
Biological speciesStreptomyces lasalocidi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWang, Q. / Kim, C.Y. / Chen, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21807088 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Mechanistic and molecular insights into iterative triepoxidation catalyzed by monooxygenase MonCI using a natural substrate analog.
Authors: Deng, Y. / Guan, Y. / Xiao, H. / Kang, Y. / Dang, D. / Jiang, G. / Wang, Q. / Yang, Y. / Cheng, L. / Zang, Y. / Zhang, S. / He, W. / Hotta, K. / Liu, J.Q. / Yang, Z. / Chen, X.
History
DepositionJul 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 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 1.2May 21, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,2129
Polymers105,2932
Non-polymers1,9187
Water8,881493
1
A: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5604
Polymers52,6471
Non-polymers9133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6525
Polymers52,6471
Non-polymers1,0054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.040, 61.970, 76.290
Angle α, β, γ (deg.)74.80, 81.86, 76.80
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 0.1 M Imidazole pH 8.0, 0.8 M NaCl, 37% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→32.943 Å / Num. obs: 67215 / % possible obs: 97.5 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.118 / Net I/σ(I): 10.18
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.016 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 4932 / CC1/2: 0.704 / Rrim(I) all: 1.096 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8T3P

8t3p


Resolution: 1.85→32.943 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 3359 5 %
Rwork0.189 --
obs0.191 67200 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→32.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6906 0 152 493 7551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077213
X-RAY DIFFRACTIONf_angle_d0.8679844
X-RAY DIFFRACTIONf_dihedral_angle_d20.892575
X-RAY DIFFRACTIONf_chiral_restr0.0571119
X-RAY DIFFRACTIONf_plane_restr0.0061291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87640.32911390.28722649X-RAY DIFFRACTION96
1.8764-1.90440.32211390.27062633X-RAY DIFFRACTION96
1.9044-1.93410.28911370.26562606X-RAY DIFFRACTION97
1.9341-1.96580.26551400.25362654X-RAY DIFFRACTION97
1.9658-1.99970.27781380.24872630X-RAY DIFFRACTION96
1.9997-2.03610.29141370.23192601X-RAY DIFFRACTION97
2.0361-2.07520.29331390.22692646X-RAY DIFFRACTION97
2.0752-2.11760.25351400.21622654X-RAY DIFFRACTION97
2.1176-2.16360.27181400.21382650X-RAY DIFFRACTION97
2.1636-2.21390.23651400.19932665X-RAY DIFFRACTION97
2.2139-2.26930.25521380.20262616X-RAY DIFFRACTION97
2.2693-2.33060.23971400.19822661X-RAY DIFFRACTION98
2.3306-2.39920.23741400.20262658X-RAY DIFFRACTION98
2.3992-2.47660.23281420.19872698X-RAY DIFFRACTION98
2.4766-2.56510.26511390.20532640X-RAY DIFFRACTION98
2.5651-2.66770.26861390.19142641X-RAY DIFFRACTION98
2.6677-2.78910.251410.19952696X-RAY DIFFRACTION98
2.7891-2.93610.24781420.18692687X-RAY DIFFRACTION98
2.9361-3.11990.20071410.18222687X-RAY DIFFRACTION99
3.1199-3.36060.21571410.17362682X-RAY DIFFRACTION99
3.3606-3.69830.20271410.162674X-RAY DIFFRACTION99
3.6983-4.23250.17751430.16072703X-RAY DIFFRACTION99
4.2325-5.32890.20671420.16162716X-RAY DIFFRACTION99
5.3289-32.9430.22021410.18332694X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 14.4962 Å / Origin y: 6.2676 Å / Origin z: 18.2828 Å
111213212223313233
T0.2032 Å20.0069 Å20.0223 Å2-0.1853 Å20.0119 Å2--0.1867 Å2
L0.1279 °20.0471 °20.1583 °2-0.2072 °20.1343 °2--0.3814 °2
S0.0061 Å °-0.011 Å °0.0082 Å °0.0537 Å °-0.012 Å °0.0354 Å °0.0169 Å °-0.0216 Å °0.0062 Å °
Refinement TLS groupSelection details: all

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