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- PDB-6ix5: The structure of LepI complex with SAM and its substrate analogue -

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Basic information

Entry
Database: PDB / ID: 6ix5
TitleThe structure of LepI complex with SAM and its substrate analogue
ComponentsO-methyltransferase lepI
KeywordsBIOSYNTHETIC PROTEIN / Leporin / SAM / O-methyltransferase / Pericyclase
Function / homology
Function and homology information


secondary metabolite biosynthetic process / O-methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-B0L / IMIDAZOLE / S-ADENOSYLMETHIONINE / O-methyltransferase lepI
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCai, Y. / Ohashi, M. / Hai, Y. / Tang, Y. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB20000000 China
CitationJournal: Nat.Chem. / Year: 2019
Title: Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI.
Authors: Cai, Y. / Hai, Y. / Ohashi, M. / Jamieson, C.S. / Garcia-Borras, M. / Houk, K.N. / Zhou, J. / Tang, Y.
History
DepositionDec 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-methyltransferase lepI
B: O-methyltransferase lepI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,96734
Polymers90,9832
Non-polymers2,98432
Water16,700927
1
A: O-methyltransferase lepI
B: O-methyltransferase lepI
hetero molecules

A: O-methyltransferase lepI
B: O-methyltransferase lepI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,93468
Polymers181,9674
Non-polymers5,96764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area31320 Å2
ΔGint-266 kcal/mol
Surface area59770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.051, 62.239, 114.150
Angle α, β, γ (deg.)90.00, 113.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein O-methyltransferase lepI / Leporins biosynthesis protein I


Mass: 45491.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (mold)
Strain: ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167
Gene: lepI, AFLA_066940 / Production host: Escherichia coli (E. coli)
References: UniProt: B8NJH3, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 8 types, 959 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-B0L / 4-hydroxy-3-[(2S,6E,8E)-2-methyldeca-6,8-dienoyl]-5-phenylpyridin-2(1H)-one


Mass: 351.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25NO3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 927 / Source method: isolated from a natural source / Formula: H2O

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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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M Magnesium chloride hexahydrate, 0.1M ADA(pH 6.5), 12%(w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 114325 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Net I/σ(I): 30.7
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.876 / Num. unique obs: 5721 / CC1/2: 0.809 / Rpim(I) all: 0.368

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Processing

Software
NameVersionClassification
PHENIXv1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXv1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IX3

6ix3


Resolution: 1.7→34.987 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1892 5579 4.99 %
Rwork0.1634 --
obs0.1647 111704 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6110 0 191 927 7228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156731
X-RAY DIFFRACTIONf_angle_d1.3439163
X-RAY DIFFRACTIONf_dihedral_angle_d25.0632577
X-RAY DIFFRACTIONf_chiral_restr0.0761007
X-RAY DIFFRACTIONf_plane_restr0.0081203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6995-1.71880.24451270.23152492X-RAY DIFFRACTION69
1.7188-1.73910.27371570.22542900X-RAY DIFFRACTION81
1.7391-1.76030.25951780.21743221X-RAY DIFFRACTION90
1.7603-1.78260.2521880.22323374X-RAY DIFFRACTION94
1.7826-1.8060.26261960.21573495X-RAY DIFFRACTION97
1.806-1.83080.24542000.20663605X-RAY DIFFRACTION99
1.8308-1.85690.23851750.20183556X-RAY DIFFRACTION99
1.8569-1.88460.23021880.19763615X-RAY DIFFRACTION100
1.8846-1.91410.25141880.21023608X-RAY DIFFRACTION100
1.9141-1.94540.25091530.20313629X-RAY DIFFRACTION100
1.9454-1.9790.22471800.17833603X-RAY DIFFRACTION100
1.979-2.0150.20892020.17353613X-RAY DIFFRACTION100
2.015-2.05370.1892000.16523611X-RAY DIFFRACTION100
2.0537-2.09560.20161730.16413589X-RAY DIFFRACTION100
2.0956-2.14120.18431890.1633608X-RAY DIFFRACTION100
2.1412-2.1910.20372000.15523611X-RAY DIFFRACTION100
2.191-2.24580.19411780.16723622X-RAY DIFFRACTION100
2.2458-2.30650.20341920.16633622X-RAY DIFFRACTION100
2.3065-2.37430.18922100.1553586X-RAY DIFFRACTION100
2.3743-2.4510.17241900.15073630X-RAY DIFFRACTION100
2.451-2.53850.18271780.15123636X-RAY DIFFRACTION100
2.5385-2.64010.18962090.15893579X-RAY DIFFRACTION100
2.6401-2.76030.18411880.15663630X-RAY DIFFRACTION100
2.7603-2.90570.18341830.15343651X-RAY DIFFRACTION100
2.9057-3.08770.16871780.15653691X-RAY DIFFRACTION100
3.0877-3.32590.16241690.15553643X-RAY DIFFRACTION100
3.3259-3.66030.15781970.15433628X-RAY DIFFRACTION100
3.6603-4.18920.17481960.13783654X-RAY DIFFRACTION100
4.1892-5.2750.13812080.1353671X-RAY DIFFRACTION100
5.275-34.99460.18172090.15693752X-RAY DIFFRACTION99

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