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- PDB-6c8r: Loganic acid O-methyltransferase complexed with SAH and loganic acid -

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Basic information

Entry
Database: PDB / ID: 6c8r
TitleLoganic acid O-methyltransferase complexed with SAH and loganic acid
ComponentsLoganic acid O-methyltransferase
KeywordsTRANSFERASE / methyltransferase / SABATH / loganic acid
Function / homology
Function and homology information


loganate O-methyltransferase / loganate O-methyltransferase activity / indole alkaloid metabolic process / methylation / metal ion binding
Similarity search - Function
SAM dependent carboxyl methyltransferase / Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Loganic acid / S-ADENOSYL-L-HOMOCYSTEINE / Loganic acid O-methyltransferase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsPetronikolou, N. / Nair, S.K.
CitationJournal: Chembiochem / Year: 2018
Title: Loganic Acid Methyltransferase: Insights into the Specificity of Methylation on an Iridoid Glycoside.
Authors: Petronikolou, N. / Hollatz, A.J. / Schuler, M.A. / Nair, S.K.
History
DepositionJan 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Loganic acid O-methyltransferase
B: Loganic acid O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4255
Polymers86,2802
Non-polymers1,1453
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-8 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.440, 116.233, 136.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Loganic acid O-methyltransferase / Loganic acid methyltransferase


Mass: 43140.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Production host: Escherichia coli (E. coli) / References: UniProt: B2KPR3
#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: Sugar ChemComp-EQV / Loganic acid / (1S,4aS,6S,7R,7aS)-1-(beta-D-glucopyranosyloxy)-6-hydroxy-7-methyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxyl ic acid


Type: D-saccharide / Mass: 376.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24O10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop / Details: 18% PEG 6000, 0.1 M MES-pH 7.0, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→116.2 Å / Num. obs: 68324 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 15.5
Reflection shellResolution: 1.951→1.957 Å / Num. unique obs: 4887 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M6E

1m6e


Resolution: 1.951→68.339 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.84
RfactorNum. reflection% reflection
Rfree0.2189 3397 4.98 %
Rwork0.1753 --
obs0.1774 68223 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.951→68.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 78 671 6479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086022
X-RAY DIFFRACTIONf_angle_d1.0738172
X-RAY DIFFRACTIONf_dihedral_angle_d14.8312245
X-RAY DIFFRACTIONf_chiral_restr0.045888
X-RAY DIFFRACTIONf_plane_restr0.0051066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9506-1.97850.25411300.24342655X-RAY DIFFRACTION100
1.9785-2.0080.29111220.23922720X-RAY DIFFRACTION100
2.008-2.03940.27521190.23642712X-RAY DIFFRACTION100
2.0394-2.07280.27511560.2222642X-RAY DIFFRACTION100
2.0728-2.10860.26931370.21322670X-RAY DIFFRACTION100
2.1086-2.14690.24261350.21562687X-RAY DIFFRACTION100
2.1469-2.18820.3251460.21092686X-RAY DIFFRACTION100
2.1882-2.23290.27251510.19452663X-RAY DIFFRACTION100
2.2329-2.28140.21421570.18952687X-RAY DIFFRACTION100
2.2814-2.33450.241250.19482709X-RAY DIFFRACTION100
2.3345-2.39290.25191560.18362676X-RAY DIFFRACTION100
2.3929-2.45760.25221280.19512714X-RAY DIFFRACTION100
2.4576-2.52990.23251630.18242691X-RAY DIFFRACTION100
2.5299-2.61160.23741570.17732662X-RAY DIFFRACTION100
2.6116-2.70490.23911230.18492410X-RAY DIFFRACTION88
2.7049-2.81320.22581540.17372685X-RAY DIFFRACTION100
2.8132-2.94130.23421400.17852728X-RAY DIFFRACTION100
2.9413-3.09630.24311300.17592746X-RAY DIFFRACTION100
3.0963-3.29030.21381550.17362678X-RAY DIFFRACTION100
3.2903-3.54430.21661610.16432720X-RAY DIFFRACTION100
3.5443-3.9010.17421370.15532778X-RAY DIFFRACTION100
3.901-4.46540.17261330.13742779X-RAY DIFFRACTION100
4.4654-5.62550.18121430.14672794X-RAY DIFFRACTION100
5.6255-68.38140.18561390.17082934X-RAY DIFFRACTION99

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