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- PDB-3p9c: Crystal structure of perennial ryegrass LpOMT1 bound to SAH -

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Basic information

Entry
Database: PDB / ID: 3p9c
TitleCrystal structure of perennial ryegrass LpOMT1 bound to SAH
ComponentsCaffeic acid O-methyltransferase
KeywordsTRANSFERASE / S-adenosylmethionine dependent O-methyltransferase
Function / homology
Function and homology information


catechol O-methyltransferase activity / catechol O-methyltransferase / 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
ACETATE ION / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / S-ADENOSYL-L-HOMOCYSTEINE / Caffeic acid O-methyltransferase
Similarity search - Component
Biological speciesLolium perenne (perennial ryegrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLouie, G.V. / Noel, J.P. / Bowman, M.E.
CitationJournal: Plant Cell / Year: 2010
Title: Structure-Function Analyses of a Caffeic Acid O-Methyltransferase from Perennial Ryegrass Reveal the Molecular Basis for Substrate Preference.
Authors: Louie, G.V. / Bowman, M.E. / Tu, Y. / Mouradov, A. / Spangenberg, G. / Noel, J.P.
History
DepositionOct 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caffeic acid O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9317
Polymers39,1471
Non-polymers7846
Water5,639313
1
A: Caffeic acid O-methyltransferase
hetero molecules

A: Caffeic acid O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,86114
Polymers78,2942
Non-polymers1,56812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area11630 Å2
ΔGint-57 kcal/mol
Surface area27510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.699, 67.699, 249.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1314-

HOH

21A-1322-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Caffeic acid O-methyltransferase


Mass: 39146.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lolium perenne (perennial ryegrass) / Gene: LpOMT1, OMT1 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZTU2, catechol O-methyltransferase

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Non-polymers , 5 types, 319 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 3.66 Å3/Da / Density % sol: 66.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 21% (w/v) PEG 8000, 0.2 M calcium acetate, 2 mM dithiothreitol, 2.5 mM S-adenosyl-L-homocysteine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2009 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.015 Å / Num. all: 66556 / Num. obs: 65047 / % possible obs: 100 % / Redundancy: 7.2 % / Rsym value: 0.116 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.93.80.4541.73012178810.454100
1.9-2.015.70.332.24278874690.33100
2.01-2.156.40.2253.24526270470.225100
2.15-2.327.60.2422.85043066250.242100
2.32-2.559.10.1574.25528860760.157100
2.55-2.8590.1285.15010255710.128100
2.85-3.298.80.1125.34372349440.112100
3.29-4.028.30.1075.53518442250.107100
4.02-5.698.50.0836.82854833650.083100
5.69-47.0158.20.06281635920060.06299.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KYZ

1kyz


Resolution: 1.8→47.015 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8467 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 3035 5.1 %random
Rwork0.2118 ---
obs-59791 99.9 %-
Solvent computationBsol: 42.7444 Å2
Displacement parametersBiso max: 75.27 Å2 / Biso mean: 26.0086 Å2 / Biso min: 6.79 Å2
Baniso -1Baniso -2Baniso -3
1--3.318 Å20 Å20 Å2
2---3.318 Å20 Å2
3---6.636 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 50 313 3034
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.193
X-RAY DIFFRACTIONc_mcbond_it1.7162
X-RAY DIFFRACTIONc_scbond_it2.7092.5
X-RAY DIFFRACTIONc_mcangle_it2.5743
X-RAY DIFFRACTIONc_scangle_it4.1814
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.760.3633590.346410981157
1.76-1.770.3343660.344811301196
1.77-1.790.2989520.315411211173
1.79-1.80.3707580.312811251183
1.8-1.810.3429650.312810971162
1.81-1.830.2921730.294611091182
1.83-1.840.3792560.303411201176
1.84-1.850.2946600.302610731133
1.85-1.870.2769560.277211651221
1.87-1.890.2827670.260311061173
1.89-1.90.2967530.269110851138
1.9-1.920.3271560.265611521208
1.92-1.930.2809610.263811201181
1.93-1.950.2606510.232411131164
1.95-1.970.2572500.244911131163
1.97-1.990.2858700.256111451215
1.99-2.010.2518690.260710711140
2.01-2.030.3105580.2511291187
2.03-2.050.2803590.253811411200
2.05-2.070.2729500.241711211171
2.07-2.10.241630.228111011164
2.1-2.120.2979480.242111541202
2.12-2.150.2333640.217710881152
2.15-2.180.2502510.215111701221
2.18-2.20.2327690.214810931162
2.2-2.240.3227560.293410961152
2.24-2.270.2228720.304110961168
2.27-2.30.2746600.221711161176
2.3-2.340.3217420.233911721214
2.34-2.380.2604430.221111061149
2.38-2.420.2671600.201211571217
2.42-2.460.1993600.188711201180
2.46-2.510.2338760.204211281204
2.51-2.560.2456690.211211021171
2.56-2.610.1968560.197711721228
2.61-2.670.2301630.208811161179
2.67-2.740.2168680.19811451213
2.74-2.820.2431650.206211541219
2.82-2.90.2247640.201511151179
2.9-2.990.2349550.218311421197
2.99-3.10.2274710.209211501221
3.1-3.220.2196660.195211581224
3.22-3.370.2161600.199511501210
3.37-3.550.1694630.191411591222
3.55-3.770.2011530.192611771230
3.77-4.060.1837780.176311531231
4.06-4.470.1694660.158811841250
4.47-5.120.1508590.164811881247
5.12-6.450.2477590.229812341293
6.45-47.0150.2144670.199213261393
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2sah.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4dtt.par
X-RAY DIFFRACTION5act_edo.par

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