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- PDB-6ix7: The structure of LepI C52A in complex with SAH and substrate analogue -

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Basic information

Entry
Database: PDB / ID: 6ix7
TitleThe structure of LepI C52A in complex with SAH and substrate analogue
ComponentsO-methyltransferase lepI
KeywordsBIOSYNTHETIC PROTEIN / Leporin / SAM / O-methyltransferase / Pericyclase
Function / homology
Function and homology information


O-methyltransferase activity / secondary metabolite biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / 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 / S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase lepI
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.835 Å
AuthorsCai, Y. / Ohashi, M. / Hai, Y. / Tang, Y. / Zhou, J.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB20000000 China
National Science Foundation (China)91856202 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)93,05717
Polymers90,9192
Non-polymers2,13815
Water12,214678
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)186,11534
Polymers181,8384
Non-polymers4,27630
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area27360 Å2
ΔGint-240 kcal/mol
Surface area58090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.281, 62.133, 113.591
Angle α, β, γ (deg.)90.00, 113.66, 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: 45459.621 Da / Num. of mol.: 2 / Mutation: C52A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167) (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 , 6 types, 693 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / 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 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 298 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: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 89126 / % possible obs: 98.7 % / Redundancy: 9.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.035 / Net I/σ(I): 35
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 1.647 / Num. unique obs: 6607 / CC1/2: 0.92 / Rpim(I) all: 0.555

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Processing

Software
NameVersionClassification
PHENIXv1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXv1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IX3

6ix3


Resolution: 1.835→32.961 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.78
RfactorNum. reflection% reflection
Rfree0.1911 2000 2.25 %
Rwork0.1807 --
obs0.181 89085 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.835→32.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 142 678 6928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076521
X-RAY DIFFRACTIONf_angle_d0.9038867
X-RAY DIFFRACTIONf_dihedral_angle_d23.0542442
X-RAY DIFFRACTIONf_chiral_restr0.052977
X-RAY DIFFRACTIONf_plane_restr0.0061164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8345-1.88040.22521430.21316209X-RAY DIFFRACTION99
1.8804-1.93130.22261430.20966236X-RAY DIFFRACTION100
1.9313-1.98810.20021420.19966221X-RAY DIFFRACTION100
1.9881-2.05220.22661450.19196281X-RAY DIFFRACTION99
2.0522-2.12560.20311420.19086197X-RAY DIFFRACTION99
2.1256-2.21070.18281440.17866243X-RAY DIFFRACTION99
2.2107-2.31120.19251420.18316201X-RAY DIFFRACTION99
2.3112-2.43310.21061400.18126099X-RAY DIFFRACTION97
2.4331-2.58540.17961390.18236034X-RAY DIFFRACTION96
2.5854-2.7850.20371440.18416308X-RAY DIFFRACTION100
2.785-3.06510.16551450.18026286X-RAY DIFFRACTION99
3.0651-3.50810.17791440.17596286X-RAY DIFFRACTION99
3.5081-4.41820.16841450.1636272X-RAY DIFFRACTION98
4.4182-32.96630.20261420.17696212X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -34.3579 Å / Origin y: -18.4677 Å / Origin z: 25.861 Å
111213212223313233
T0.1335 Å2-0.0181 Å2-0.0118 Å2-0.1046 Å20.034 Å2--0.1015 Å2
L1.1163 °2-0.4893 °2-0.1272 °2-0.4486 °20.0607 °2--0.3654 °2
S-0.0081 Å °0.1098 Å °0.0936 Å °0.003 Å °-0.0198 Å °-0.0295 Å °-0.0309 Å °-0.0226 Å °0.0227 Å °
Refinement TLS groupSelection details: all

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