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- PDB-8up4: Crystal structure of Lsd18 (a flavin-dependent monooxygenase) -

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Basic information

Entry
Database: PDB / ID: 8up4
TitleCrystal structure of Lsd18 (a flavin-dependent monooxygenase)
ComponentsFlavin-dependent monooxygenase Lsd18
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: 1.51 Å
AuthorsWang, Q. / Chen, X. / Kim, C.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
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
DepositionOct 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: 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

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Assembly

Deposited unit
A: Flavin-dependent monooxygenase Lsd18
B: Flavin-dependent monooxygenase Lsd18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9356
Polymers105,2932
Non-polymers1,6424
Water16,195899
1
A: Flavin-dependent monooxygenase Lsd18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4683
Polymers52,6471
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flavin-dependent monooxygenase Lsd18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4683
Polymers52,6471
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.354, 61.790, 75.355
Angle α, β, γ (deg.)74.64, 81.70, 77.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Flavin-dependent monooxygenase 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 / Production host: Escherichia coli (E. coli) / References: UniProt: B5M9L6
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 899 / 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: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH8.5, 0.85 M NaCl, 32% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→58.45 Å / Num. obs: 117632 / % possible obs: 95.9 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 11.6
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 16922 / CC1/2: 0.871 / Rpim(I) all: 0.266 / Rrim(I) all: 0.496 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→36.749 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1785 5763 4.89 %
Rwork0.1401 --
obs0.142 117632 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→36.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7104 0 2 899 8005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097331
X-RAY DIFFRACTIONf_angle_d1.02210007
X-RAY DIFFRACTIONf_dihedral_angle_d22.1162661
X-RAY DIFFRACTIONf_chiral_restr0.0891129
X-RAY DIFFRACTIONf_plane_restr0.0071320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.52720.27951850.19623652X-RAY DIFFRACTION94
1.5272-1.54510.2521730.18663750X-RAY DIFFRACTION94
1.5451-1.5640.25881960.17633591X-RAY DIFFRACTION94
1.564-1.58380.21121910.16963680X-RAY DIFFRACTION94
1.5838-1.60460.21271950.1573688X-RAY DIFFRACTION95
1.6046-1.62660.19511960.15083694X-RAY DIFFRACTION94
1.6266-1.64980.22051780.14583696X-RAY DIFFRACTION95
1.6498-1.67450.18291910.14263735X-RAY DIFFRACTION95
1.6745-1.70060.18541880.13543655X-RAY DIFFRACTION95
1.7006-1.72850.20171890.14043700X-RAY DIFFRACTION95
1.7285-1.75830.22782040.14013748X-RAY DIFFRACTION95
1.7583-1.79030.20192050.1413691X-RAY DIFFRACTION96
1.7903-1.82470.18362170.1383683X-RAY DIFFRACTION96
1.8247-1.8620.18031990.12993761X-RAY DIFFRACTION96
1.862-1.90240.17741930.13363711X-RAY DIFFRACTION96
1.9024-1.94670.20281930.13183778X-RAY DIFFRACTION96
1.9467-1.99540.18121780.13473760X-RAY DIFFRACTION96
1.9954-2.04930.20011900.12883758X-RAY DIFFRACTION97
2.0493-2.10960.18582220.12683763X-RAY DIFFRACTION97
2.1096-2.17770.17241830.12973775X-RAY DIFFRACTION97
2.1777-2.25550.17311840.13013758X-RAY DIFFRACTION97
2.2555-2.34580.18441880.13343808X-RAY DIFFRACTION97
2.3458-2.45260.17981840.13883797X-RAY DIFFRACTION97
2.4526-2.58180.19591860.14643815X-RAY DIFFRACTION97
2.5818-2.74350.18971820.15253809X-RAY DIFFRACTION97
2.7435-2.95530.19011890.15363770X-RAY DIFFRACTION97
2.9553-3.25250.1771750.14433807X-RAY DIFFRACTION97
3.2525-3.72280.15592040.13143731X-RAY DIFFRACTION97
3.7228-4.68880.13552070.12453761X-RAY DIFFRACTION96
4.6888-36.7490.16651980.15183756X-RAY DIFFRACTION97

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