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- PDB-6ix8: The structure of LepI C52A in complex with SAM and its substrate ... -

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Basic information

Entry
Database: PDB / ID: 6ix8
TitleThe structure of LepI C52A in complex with SAM and its 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 / Plant 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
ACETATE ION / Chem-B3O / S-ADENOSYLMETHIONINE / O-methyltransferase lepI
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.659 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)92,90518
Polymers90,9192
Non-polymers1,98616
Water12,412689
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)185,81036
Polymers181,8384
Non-polymers3,97232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area25260 Å2
ΔGint-275 kcal/mol
Surface area59290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.800, 62.562, 113.836
Angle α, β, γ (deg.)90.00, 113.34, 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 , 7 types, 705 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-B3O / (1R,2R,4aS,8S,8aR)-2,8-dimethyl-5'-phenyl-4a,5,6,7,8,8a-hexahydro-2H,2'H-spiro[naphthalene-1,3'-pyridine]-2',4'(1'H)-dione


Mass: 335.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25NO2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 59.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium chloride, 0.1M MES(pH 6), 20%(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 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.658→50 Å / Num. obs: 122483 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.8
Reflection shellResolution: 1.658→1.69 Å / Rmerge(I) obs: 1.072 / Num. unique obs: 4777 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IX3

6ix3


Resolution: 1.659→28.802 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.18
RfactorNum. reflection% reflection
Rfree0.1972 5905 5.03 %
Rwork0.1677 --
obs0.1692 117502 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.659→28.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 131 689 6928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0186586
X-RAY DIFFRACTIONf_angle_d1.4969002
X-RAY DIFFRACTIONf_dihedral_angle_d9.0565465
X-RAY DIFFRACTIONf_chiral_restr0.0941006
X-RAY DIFFRACTIONf_plane_restr0.011176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6588-1.67760.27721140.24372310X-RAY DIFFRACTION60
1.6776-1.69730.25581420.22872787X-RAY DIFFRACTION72
1.6973-1.7180.28291510.22473047X-RAY DIFFRACTION80
1.718-1.73980.2531800.22363333X-RAY DIFFRACTION85
1.7398-1.76270.24132140.21833488X-RAY DIFFRACTION90
1.7627-1.78680.24952170.20983546X-RAY DIFFRACTION92
1.7868-1.81230.25622020.20433669X-RAY DIFFRACTION96
1.8123-1.83940.22262260.19183733X-RAY DIFFRACTION96
1.8394-1.86810.22952340.18753793X-RAY DIFFRACTION99
1.8681-1.89880.22812020.18743822X-RAY DIFFRACTION99
1.8988-1.93150.23441890.18753878X-RAY DIFFRACTION99
1.9315-1.96660.21292090.18133866X-RAY DIFFRACTION99
1.9666-2.00440.2221840.18193871X-RAY DIFFRACTION100
2.0044-2.04530.20251960.17473871X-RAY DIFFRACTION100
2.0453-2.08980.20432060.16743881X-RAY DIFFRACTION100
2.0898-2.13840.18181900.16683876X-RAY DIFFRACTION100
2.1384-2.19180.20621920.16343895X-RAY DIFFRACTION100
2.1918-2.25110.22712120.16253899X-RAY DIFFRACTION100
2.2511-2.31730.19912120.16353884X-RAY DIFFRACTION100
2.3173-2.39210.19162020.16023893X-RAY DIFFRACTION100
2.3921-2.47750.18841900.15993903X-RAY DIFFRACTION100
2.4775-2.57660.20422070.16073872X-RAY DIFFRACTION100
2.5766-2.69380.20041790.16643944X-RAY DIFFRACTION100
2.6938-2.83570.21911860.16673909X-RAY DIFFRACTION100
2.8357-3.01320.17682040.16163919X-RAY DIFFRACTION100
3.0132-3.24560.17362310.16633880X-RAY DIFFRACTION100
3.2456-3.57170.20371940.16483920X-RAY DIFFRACTION100
3.5717-4.08720.16192120.15053938X-RAY DIFFRACTION100
4.0872-5.14470.15661800.13653962X-RAY DIFFRACTION100
5.1447-28.80620.16092480.15674008X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -34.1338 Å / Origin y: -18.1989 Å / Origin z: 26.0453 Å
111213212223313233
T0.0461 Å2-0.0028 Å2-0.0019 Å2-0.0227 Å20.0202 Å2--0.0357 Å2
L0.4778 °2-0.2209 °20.0336 °2-0.1749 °20.0064 °2--0.1953 °2
S-0.0259 Å °0.0716 Å °0.0167 Å °0.0205 Å °-0.0102 Å °-0.0021 Å °-0.0114 Å °-0.0161 Å °-0.0264 Å °
Refinement TLS groupSelection details: all

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