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- PDB-6j46: LepI-SAH complex structure -

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Basic information

Entry
Database: PDB / ID: 6j46
TitleLepI-SAH complex structure
ComponentsO-methyltransferase lepI
KeywordsTRANSFERASE / Complex
Function / homology
Function and homology information


secondary metabolite biosynthetic process / O-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
S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase lepI
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.621 Å
AuthorsQiu, S. / Wei, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21702141 China
CitationJournal: Signal Transduct Target Ther / Year: 2019
Title: Deciphering the regulatory and catalytic mechanisms of an unusual SAM-dependent enzyme.
Authors: Sun, Q. / Hu, Y. / Gu, Y. / Huang, J. / He, J. / Luo, L. / Yang, Y. / Yin, S. / Dou, C. / Wang, T. / Fu, X. / He, L. / Qi, S. / Zhu, X. / Yang, S. / Wei, X. / Cheng, W.
History
DepositionJan 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

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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)87,4984
Polymers86,7292
Non-polymers7692
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-75 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.817, 62.333, 112.735
Angle α, β, γ (deg.)90.00, 112.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 43364.492 Da / Num. of mol.: 2
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 BL21(DE3) (bacteria)
References: UniProt: B8NJH3, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.10M bis-tris pH 7.0, 35% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.621→53.202 Å / Num. obs: 28684 / % possible obs: 91.68 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.4
Reflection shellResolution: 2.621→2.621 Å / Rmerge(I) obs: 0.827 / Num. unique obs: 14091

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J1O

6j1o


Resolution: 2.621→53.202 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1413 4.95 %
Rwork0.2087 --
obs0.2105 28554 91.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.621→53.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 52 20 6158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036339
X-RAY DIFFRACTIONf_angle_d0.5838623
X-RAY DIFFRACTIONf_dihedral_angle_d17.583885
X-RAY DIFFRACTIONf_chiral_restr0.041965
X-RAY DIFFRACTIONf_plane_restr0.0041126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6207-2.71440.436610.3941850X-RAY DIFFRACTION30
2.7144-2.8230.3511730.28732889X-RAY DIFFRACTION99
2.823-2.95150.2991450.27572926X-RAY DIFFRACTION99
2.9515-3.10710.31931360.26052911X-RAY DIFFRACTION99
3.1071-3.30180.29311460.25432931X-RAY DIFFRACTION99
3.3018-3.55660.26411230.24922821X-RAY DIFFRACTION95
3.5566-3.91450.24381790.20832928X-RAY DIFFRACTION100
3.9145-4.48060.19621550.18682947X-RAY DIFFRACTION100
4.4806-5.64410.24751570.18752965X-RAY DIFFRACTION99
5.6441-53.2130.20271380.17352973X-RAY DIFFRACTION97

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