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- PDB-6iv7: The crystal structure of a SAM-dependent enzyme from aspergillus ... -

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Basic information

Entry
Database: PDB / ID: 6iv7
TitleThe crystal structure of a SAM-dependent enzyme from aspergillus flavus
Componentsmethyltransferase lepI
KeywordsTRANSFERASE / SAM / O-methyltransferase
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
S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase lepI
Similarity search - Component
Biological speciesAspergillus flavus NRRL3357 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.937 Å
AuthorsZhou, Y.Z. / Peng, T. / Liao, L.J. / Liu, X.K. / Zhao, Y.C. / Guo, Y. / Zeng, Z.X.
CitationJournal: To Be Published
Title: The crystal structure of A SAM-Dependent enzyme from Aspergillus flavus
Authors: Zhou, Y.Z. / Peng, T. / Liao, L.J. / Zhao, Y.C. / Liu, X.K. / Guo, Y. / Zeng, Z.X.
History
DepositionDec 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: methyltransferase lepI
B: methyltransferase lepI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2354
Polymers86,4672
Non-polymers7692
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-74 kcal/mol
Surface area30690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.556, 62.225, 113.354
Angle α, β, γ (deg.)90.000, 113.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein methyltransferase lepI / Leporins biosynthesis protein I


Mass: 43233.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus NRRL3357 (mold)
Strain: ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167
Gene: lepI, AFLA_066940 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.05M CaCl2, 0.1M Bis-Tris PH 6.5, 30% mPEG 550 / PH range: 6.0-7.0

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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: Mar 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.937→75.91 Å / Num. obs: 72748 / % possible obs: 94.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 35.62 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.058 / Rrim(I) all: 0.109 / Net I/σ(I): 2.15
Reflection shellResolution: 1.94→1.94 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.869 / Num. unique obs: 11076 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIX1.14_3260phasing
RefinementMethod to determine structure: SAD / Resolution: 1.937→41.881 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 3628 5 %Random
Rwork0.2024 ---
obs0.2041 72590 94.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.48 Å2 / Biso mean: 41.3624 Å2 / Biso min: 11.98 Å2
Refinement stepCycle: final / Resolution: 1.937→41.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6070 0 52 186 6308
Biso mean--39.31 41.54 -
Num. residues----772
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9371-1.96260.32541620.28612742290499
1.9626-1.98950.31961330.27982789292299
1.9895-2.01790.32791520.26972769292199
2.0179-2.0480.31871540.27322742289699
2.048-2.080.3993630.30561123118640
2.08-2.11410.31741420.27412564270694
2.1141-2.15060.27831330.24492696282995
2.1506-2.18970.30441390.22742756289599
2.1897-2.23180.24981410.233327822923100
2.2318-2.27730.3573820.24091569165156
2.2773-2.32690.23991540.22412767292199
2.3269-2.3810.26381680.21992742291099
2.381-2.44050.28871710.21632754292599
2.4405-2.50650.23711220.20982809293199
2.5065-2.58020.25961310.22032808293999
2.5802-2.66350.28971390.2192756289599
2.6635-2.75870.26441470.21032775292299
2.7587-2.86910.2571270.2222811293899
2.8691-2.99970.25341340.22532735286998
2.9997-3.15780.24741390.22812687282696
3.1578-3.35550.30581290.225128172946100
3.3555-3.61450.24261540.205927982952100
3.6145-3.9780.21741580.18062791294999
3.978-4.5530.19621450.15692807295298
4.553-5.73390.19091560.17262745290197
5.7339-41.89060.18511530.17482828298197

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