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- PDB-8wvt: Crystal structure of Lsd18 in complex with ligands -

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Basic information

Entry
Database: PDB / ID: 8wvt
TitleCrystal structure of Lsd18 in complex with ligands
ComponentsPutative epoxidase LasC
KeywordsFLAVOPROTEIN / FAD-dependent monooxygenase / epoxidase
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 / : / Putative epoxidase LasC
Similarity search - Component
Biological speciesStreptomyces lasalocidi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDeng, Y.M. / Hu, Y.L. / Chen, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21807088 China
CitationJournal: To Be Published
Title: Crystal structure of Lsd18 in complex with ligands
Authors: Deng, Y.M. / Hu, Y.L. / Chen, X.
History
DepositionOct 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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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)108,20312
Polymers105,2932
Non-polymers2,91010
Water14,520806
1
A: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1106
Polymers52,6471
Non-polymers1,4635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0946
Polymers52,6471
Non-polymers1,4475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.921, 61.804, 75.633
Angle α, β, γ (deg.)74.61, 81.74, 76.79
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative epoxidase LasC


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

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Non-polymers , 6 types, 816 molecules

#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-X9E / (4R,5S)-3-((2R,3S,4S,E)-2,6-diethyl-9-((2R,3R)-2-ethyl-3-methyloxiran-2-yl)-3-hydroxy-4-methylnon-6-enoyl)-4-methyl-5-phenyloxazolidin-2-one


Mass: 485.655 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H43NO5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-A1LWM / (4R,5S)-4-methyl-5-phenyl-3-((2R,3S,4S,6E,10E)-2,6,10-triethyl-3-hydroxy-4-methyldodeca-6,10-dienoyl)oxazolidin-2-one


Mass: 469.656 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H43NO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 291 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: Jun 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→25.284 Å / Num. obs: 76354 / % possible obs: 95.26 % / Redundancy: 1 % / CC1/2: 0.885 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.145 / Rrim(I) all: 0.206 / Net I/σ(I): 8.5
Reflection shellResolution: 1.75→1.813 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3815 / CC1/2: 0.8 / Rpim(I) all: 0.528 / Rrim(I) all: 0.293 / % possible all: 86.63

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8UP4

8up4


Resolution: 1.75→25.284 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 3773 4.94 %
Rwork0.2085 --
obs0.2105 76322 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→25.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6899 0 153 806 7858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077193
X-RAY DIFFRACTIONf_angle_d0.8559817
X-RAY DIFFRACTIONf_dihedral_angle_d20.1762559
X-RAY DIFFRACTIONf_chiral_restr0.0541121
X-RAY DIFFRACTIONf_plane_restr0.0061285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77220.29431090.23852412X-RAY DIFFRACTION86
1.7722-1.79550.27551210.23332447X-RAY DIFFRACTION86
1.7955-1.82010.32531470.22682476X-RAY DIFFRACTION88
1.8201-1.84610.26211200.22362506X-RAY DIFFRACTION89
1.8461-1.87360.2751570.21422584X-RAY DIFFRACTION91
1.8736-1.90290.25611240.2182592X-RAY DIFFRACTION94
1.9029-1.93410.30311340.22722705X-RAY DIFFRACTION95
1.9341-1.96740.27011440.22412664X-RAY DIFFRACTION95
1.9674-2.00320.32931420.21882714X-RAY DIFFRACTION96
2.0032-2.04170.28591420.20252727X-RAY DIFFRACTION96
2.0417-2.08330.30261520.2062660X-RAY DIFFRACTION96
2.0833-2.12860.23011380.20682754X-RAY DIFFRACTION96
2.1286-2.17810.25711400.2062694X-RAY DIFFRACTION96
2.1781-2.23250.26961520.20932730X-RAY DIFFRACTION97
2.2325-2.29280.23851470.2092720X-RAY DIFFRACTION97
2.2928-2.36030.2581430.20942733X-RAY DIFFRACTION97
2.3603-2.43640.24231230.21482766X-RAY DIFFRACTION97
2.4364-2.52340.2781470.21222739X-RAY DIFFRACTION98
2.5234-2.62430.2811350.21452805X-RAY DIFFRACTION98
2.6243-2.74360.23311470.21642736X-RAY DIFFRACTION98
2.7436-2.88810.24271420.21912749X-RAY DIFFRACTION98
2.8881-3.06870.23531580.21952764X-RAY DIFFRACTION98
3.0687-3.30520.25381500.20342766X-RAY DIFFRACTION98
3.3052-3.6370.21821340.20022783X-RAY DIFFRACTION98
3.637-4.16120.23561390.18712757X-RAY DIFFRACTION98
4.1612-5.2350.20221440.18762797X-RAY DIFFRACTION99
5.235-25.2840.20251420.20962769X-RAY DIFFRACTION98

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