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- PDB-8wvb: Crystal structure of Lsd18 mutant S195M -

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Basic information

Entry
Database: PDB / ID: 8wvb
TitleCrystal structure of Lsd18 mutant 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: 2.5 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)107,0246
Polymers105,3822
Non-polymers1,6424
Water3,333185
1
A: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5123
Polymers52,6911
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative epoxidase LasC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5123
Polymers52,6911
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.041, 48.671, 136.049
Angle α, β, γ (deg.)90.00, 91.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative epoxidase LasC


Mass: 52690.812 Da / Num. of mol.: 2 / Mutation: 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
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
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: 39.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→30.114 Å / Num. obs: 28322 / % possible obs: 99.03 % / Redundancy: 6.7 % / CC1/2: 0.918 / Rmerge(I) obs: 0.37 / Rpim(I) all: 0.153 / Rrim(I) all: 0.402 / Net I/σ(I): 3.9
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.994 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2798 / CC1/2: 0.783 / Rpim(I) all: 0.408 / Rrim(I) all: 1.077 / % possible all: 98.52

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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: 2.5→30.114 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 1361 4.81 %
Rwork0.2089 --
obs0.211 28317 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→30.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6790 0 108 185 7083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037038
X-RAY DIFFRACTIONf_angle_d0.5499621
X-RAY DIFFRACTIONf_dihedral_angle_d16.4982471
X-RAY DIFFRACTIONf_chiral_restr0.0421112
X-RAY DIFFRACTIONf_plane_restr0.0041257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58940.27421240.2372673X-RAY DIFFRACTION99
2.5894-2.6930.31431460.25162689X-RAY DIFFRACTION100
2.693-2.81540.30941260.25752662X-RAY DIFFRACTION99
2.8154-2.96380.30021420.24342657X-RAY DIFFRACTION100
2.9638-3.14930.30311410.23032691X-RAY DIFFRACTION100
3.1493-3.39210.24131430.22672678X-RAY DIFFRACTION99
3.3921-3.73290.26071260.18882689X-RAY DIFFRACTION99
3.7329-4.27180.22851310.18082681X-RAY DIFFRACTION98
4.2718-5.3770.18681440.17262753X-RAY DIFFRACTION100
5.377-30.1140.21721380.19042783X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.4543 Å / Origin y: 9.3309 Å / Origin z: 33.7537 Å
111213212223313233
T0.0998 Å2-0.0164 Å2-0.0115 Å2-0.0977 Å2-0.0051 Å2--0.1864 Å2
L0.1845 °2-0.1405 °20.1219 °2-0.1287 °2-0.0289 °2--0.2407 °2
S-0.0217 Å °-0.0168 Å °0.017 Å °-0.01 Å °0.014 Å °-0.0135 Å °-0.0326 Å °-0.0192 Å °0.0115 Å °
Refinement TLS groupSelection details: all

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