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- PDB-5cvj: Monolignol 4-O-methyltransferase 5 - coniferyl alcohol -

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Basic information

Entry
Database: PDB / ID: 5cvj
TitleMonolignol 4-O-methyltransferase 5 - coniferyl alcohol
Components(Iso)eugenol O-methyltransferase(Iso)eugenol O-methyltransferase
KeywordsTRANSFERASE / Monolignol 4-O-methyltransferase / lignin / S-ADENOSYL-L-HOMOCYSTEINE / coniferyl alcohol
Function / homology
Function and homology information


(iso)eugenol O-methyltransferase / (iso)eugenol O-methyltransferase activity / S-adenosyl-L-methionine:eugenol-O-methyltransferase activity / organic substance metabolic process / 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 / NITRATE ION / S-ADENOSYL-L-HOMOCYSTEINE / (Iso)eugenol O-methyltransferase
Similarity search - Component
Biological speciesClarkia breweri (fairy fans)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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 at 1.68 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 1.1Dec 4, 2019Group: 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 1.2Mar 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
D: (Iso)eugenol O-methyltransferase
A: (Iso)eugenol O-methyltransferase
B: (Iso)eugenol O-methyltransferase
C: (Iso)eugenol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,54330
Polymers160,1694
Non-polymers3,37526
Water14,970831
1
D: (Iso)eugenol O-methyltransferase
B: (Iso)eugenol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,89617
Polymers80,0842
Non-polymers1,81115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-65 kcal/mol
Surface area27120 Å2
MethodPISA
2
A: (Iso)eugenol O-methyltransferase
C: (Iso)eugenol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,64813
Polymers80,0842
Non-polymers1,56311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-64 kcal/mol
Surface area27520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.070, 150.360, 67.930
Angle α, β, γ (deg.)90.00, 93.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40042.215 Da / Num. of mol.: 4
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 / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S
#3: Chemical
ChemComp-N7I / 4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol / Coniferyl alcohol / Coniferyl alcohol


Mass: 180.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12O3
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 831 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Crystals of both MOMT5 were 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 monolignols
PH range: 7.0 - 7.4

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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 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.68→75.18 Å / Num. obs: 146779 / % possible obs: 97.8 % / Redundancy: 5.7 % / Net I/σ(I): 14.6
Reflection shellResolution: 1.6→1.77 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.6 / % possible all: 85.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementResolution: 1.8→75.18 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.212 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18003 6130 5 %RANDOM
Rwork0.15091 ---
obs0.15234 115976 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å21.09 Å2
2--0.03 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→75.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10981 0 228 831 12040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01911470
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210969
X-RAY DIFFRACTIONr_angle_refined_deg2.1761.99415579
X-RAY DIFFRACTIONr_angle_other_deg1.1743.00125355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22551428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94524.766428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.743151867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5481528
X-RAY DIFFRACTIONr_chiral_restr0.1510.21765
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02112742
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022402
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_it2.351.9745735
X-RAY DIFFRACTIONr_mcbond_other2.351.9745734
X-RAY DIFFRACTIONr_mcangle_it3.4112.9477155
X-RAY DIFFRACTIONr_mcangle_other3.4112.9477156
X-RAY DIFFRACTIONr_scbond_it3.4862.3275735
X-RAY DIFFRACTIONr_scbond_other3.4462.3165682
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0313.3288371
X-RAY DIFFRACTIONr_long_range_B_refined6.51316.63513683
X-RAY DIFFRACTIONr_long_range_B_other6.4716.41213312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 443 -
Rwork0.195 8580 -
obs--99.97 %

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