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- PDB-5cvv: coniferyl alcohol bound monolignol 4-O-methyltransferase 9 -

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Basic information

Entry
Database: PDB / ID: 5cvv
Titleconiferyl alcohol bound monolignol 4-O-methyltransferase 9
Components(Iso)eugenol O-methyltransferase
KeywordsTRANSFERASE / monolignol-4-O methyltransferase / lignin / coniferyl alcohol / s-adenosylmethionine
Function / homology
Function and homology information


(iso)eugenol O-methyltransferase / (iso)eugenol O-methyltransferase activity / S-adenosyl-L-methionine:eugenol-O-methyltransferase activity / : / S-adenosylmethionine-dependent methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol / S-ADENOSYL-L-HOMOCYSTEINE / (Iso)eugenol O-methyltransferase
Similarity search - Component
Biological speciesClarkia breweri (fairy fans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.73 Å
AuthorsCai, Y. / Liu, C.-J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DEAC0298CH10886 United States
CitationJournal: To Be Published
Title: Structure of coniferyl alcohol bound monolignol 4-O-methyltransferase 9 at 1.73 Angstroms resolution
Authors: Cai, Y. / Liu, C.-J.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 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: (Iso)eugenol O-methyltransferase
B: (Iso)eugenol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2245
Polymers80,2752
Non-polymers9493
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-64 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.290, 67.480, 74.070
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein (Iso)eugenol O-methyltransferase / S-adenosysl-L-methionine:(Iso)eugenol O-methyltransferase / IEMT


Mass: 40137.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clarkia breweri (fairy fans) / Gene: IEMT1 / Production host: Escherichia coli (E. coli)
References: UniProt: O04385, (iso)eugenol O-methyltransferase
#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-N7I / 4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol / Coniferyl alcohol


Mass: 180.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: MOMT9 was grown via a hanging-drop vapor diffusion method in 22% (w/v) PEG 4000, 0.3 M Mg(NO3)2 (pH 7.2), and 1 mM DTT with 1 mM SAH and 1 mM coniferyl alcohol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.73→73.96 Å / Num. obs: 70249 / % possible obs: 100 % / Redundancy: 5.84 % / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 1.73→73.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.348 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21249 3541 5 %RANDOM
Rwork0.18127 ---
obs0.18284 66671 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å2-0.69 Å2
2---0.44 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.73→73.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5375 0 65 273 5713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0195570
X-RAY DIFFRACTIONr_bond_other_d0.0030.025346
X-RAY DIFFRACTIONr_angle_refined_deg2.251.9887570
X-RAY DIFFRACTIONr_angle_other_deg1.16312349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20724.554213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46915911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.971516
X-RAY DIFFRACTIONr_chiral_restr0.1460.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216185
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021185
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0832.5892798
X-RAY DIFFRACTIONr_mcbond_other3.0832.5882797
X-RAY DIFFRACTIONr_mcangle_it4.1683.8623487
X-RAY DIFFRACTIONr_mcangle_other4.1683.8623488
X-RAY DIFFRACTIONr_scbond_it4.0872.9882772
X-RAY DIFFRACTIONr_scbond_other4.0872.9892773
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9314.3184084
X-RAY DIFFRACTIONr_long_range_B_refined7.31321.356486
X-RAY DIFFRACTIONr_long_range_B_other7.321.2336399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 254 -
Rwork0.255 4891 -
obs--99.9 %

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