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- PDB-3p9k: Crystal structure of perennial ryegrass LpOMT1 complexed with S-a... -

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Basic information

Entry
Database: PDB / ID: 3p9k
TitleCrystal structure of perennial ryegrass LpOMT1 complexed with S-adenosyl-L-homocysteine and coniferaldehyde
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
(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal / 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: 2.25 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

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Assembly

Deposited unit
A: Caffeic acid O-methyltransferase
B: Caffeic acid O-methyltransferase
C: Caffeic acid O-methyltransferase
D: Caffeic acid O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,83712
Polymers156,5874
Non-polymers2,2508
Water5,657314
1
A: Caffeic acid O-methyltransferase
B: Caffeic acid O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4196
Polymers78,2942
Non-polymers1,1254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-64 kcal/mol
Surface area26850 Å2
MethodPISA
2
C: Caffeic acid O-methyltransferase
D: Caffeic acid O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4196
Polymers78,2942
Non-polymers1,1254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-61 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.375, 85.062, 98.586
Angle α, β, γ (deg.)90.000, 111.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Caffeic acid O-methyltransferase


Mass: 39146.754 Da / Num. of mol.: 4
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
#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: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-CIY / (2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal / Coniferaldehyde / Coniferyl aldehyde


Mass: 178.185 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium succinate, 28% (w/v) PEG 5000 monomethylether, 2 mM dithiothreitol, 2.5 mM S-adenosyl-L-homocysteine, 5 mM coniferaldehyde, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2008 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.693 Å / Num. obs: 78617 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rsym value: 0.118 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.372.90.4391.32834799200.43998.1
2.37-2.523.20.31923010895560.319100
2.52-2.693.70.292.13349289730.2999.9
2.69-2.93.90.2092.93291884090.20999.9
2.9-3.183.90.1523.83025577380.15299.9
3.18-3.563.90.1114.72701469720.11199.7
3.56-4.113.80.0865.62351661700.08699.6
4.11-5.033.60.07361908452400.07399.8
5.03-7.123.90.0686.61570340750.06899.9
7.12-48.6933.90.0586.9898522880.05899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P9I
Resolution: 2.25→48.693 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7169 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3952 5 %random
Rwork0.2316 ---
obs-78617 98.6 %-
Solvent computationBsol: 30.688 Å2
Displacement parametersBiso max: 107.12 Å2 / Biso mean: 34.915 Å2 / Biso min: 3.21 Å2
Baniso -1Baniso -2Baniso -3
1-10.832 Å20 Å2-1.096 Å2
2---23.019 Å20 Å2
3---12.187 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10760 0 156 314 11230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.214
X-RAY DIFFRACTIONc_mcbond_it1.9642
X-RAY DIFFRACTIONc_scbond_it3.1232.5
X-RAY DIFFRACTIONc_mcangle_it3.0523
X-RAY DIFFRACTIONc_scangle_it4.5614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.25-2.350.36234070.354580088415
2.35-2.480.32414260.29982218647
2.48-2.630.31774500.274381988648
2.63-2.830.29694430.254782598702
2.83-3.120.28054750.236182008675
3.12-3.570.27544160.226882538669
3.57-4.50.20824210.18883008721
4.5-48.6930.2154490.196483938842
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2sah.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4cfh.par

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