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- PDB-8wvf: Crystal structure of Lsd18 mutant T189M and S195M -

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Basic information

Entry
Database: PDB / ID: 8wvf
TitleCrystal structure of Lsd18 mutant T189M and S195M
ComponentsPutative epoxidase LasC
KeywordsFLAVOPROTEIN / FAD dependent monooxygenase / epoxidase / mutant
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: 3.757 Å
AuthorsLiu, N. / Xiao, H.L. / Chen, X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2106100 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Simultaneous Improvement in the Thermostability and Catalytic Activity of Epoxidase Lsd18 for the Synthesis of Lasalocid A.
Authors: Liu, N. / Xiao, H. / Zang, Y. / Zhou, L. / Mencius, J. / Yang, Z. / Quan, S. / Chen, X.
History
DepositionOct 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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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)107,0134
Polymers105,4422
Non-polymers1,5712
Water0
1
A: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5062
Polymers52,7211
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5062
Polymers52,7211
Non-polymers7861
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.005, 48.116, 135.569
Angle α, β, γ (deg.)90.00, 91.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative epoxidase LasC


Mass: 52720.906 Da / Num. of mol.: 2 / Mutation: T189M,S195M
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 / 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
Has ligand of interestY

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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: 39.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.2 M Li2SO4, 0.1M Tris, pH 7.5, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Oct 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.757→20.044 Å / Num. obs: 7514 / % possible obs: 87.95 % / Redundancy: 1 % / CC1/2: 0.87 / Rmerge(I) obs: 0.268 / Rpim(I) all: 0.165 / Rrim(I) all: 0.317 / Net I/σ(I): 3.7
Reflection shellResolution: 3.757→3.897 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 689 / CC1/2: 0.805 / Rpim(I) all: 0.266 / Rrim(I) all: 0.473

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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
PDB Unreleased entry


Resolution: 3.757→20.044 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3191 377 5.02 %
Rwork0.232 --
obs0.2365 7514 88.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.757→20.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6623 0 0 0 6623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026766
X-RAY DIFFRACTIONf_angle_d0.5659301
X-RAY DIFFRACTIONf_dihedral_angle_d5.1453922
X-RAY DIFFRACTIONf_chiral_restr0.0411106
X-RAY DIFFRACTIONf_plane_restr0.0051214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.757-4.29550.31731020.23772213X-RAY DIFFRACTION83
4.2955-5.39430.30171440.22142285X-RAY DIFFRACTION86
5.3943-20.0440.33981310.2372639X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 14.6083 Å / Origin y: 9.313 Å / Origin z: 33.4028 Å
111213212223313233
T0.2459 Å20.0122 Å20.0023 Å2-0.151 Å20.0129 Å2--0.2227 Å2
L0.2007 °2-0.0599 °20.157 °2-0.0922 °20.0071 °2--0.2491 °2
S0.0053 Å °0.0214 Å °-0.0201 Å °-0.0122 Å °0.0273 Å °-0.0003 Å °-0.0685 Å °-0.0016 Å °-0.0209 Å °
Refinement TLS groupSelection details: all

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