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- PDB-3c3y: Crystal Structure of PFOMT, Phenylpropanoid and Flavonoid O-methy... -

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Basic information

Entry
Database: PDB / ID: 3c3y
TitleCrystal Structure of PFOMT, Phenylpropanoid and Flavonoid O-methyltransferase from M. crystallinum
ComponentsO-methyltransferase
KeywordsTRANSFERASE / plant secondary metabolism / O-methyltransferase
Function / homology
Function and homology information


caffeoyl-CoA O-methyltransferase / caffeoyl-CoA O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase
Similarity search - Component
Biological speciesMesembryanthemum crystallinum (common iceplant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.371 Å
AuthorsKopycki, J.G. / Rauh, D. / Neumann, P. / Stubbs, M.T.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Biochemical and Structural Analysis of Substrate Promiscuity in Plant Mg(2+)-Dependent O-Methyltransferases
Authors: Kopycki, J.G. / Rauh, D. / Chumanevich, A.A. / Neumann, P. / Vogt, T. / Stubbs, M.T.
History
DepositionJan 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: O-methyltransferase
B: O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1267
Polymers53,2372
Non-polymers8895
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-58.1 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.890, 71.830, 128.120
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 O-methyltransferase / PFOMT


Mass: 26618.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesembryanthemum crystallinum (common iceplant)
Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 pREP4
References: UniProt: Q6YI95, caffeoyl-CoA O-methyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 4000, 0.2M CaCl2, 100mM HEPES/NaOH, pH 7.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW611.05
SYNCHROTRONMPG/DESY, HAMBURG BW620.97905 0.9500
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMay 20, 2004
MARRESEARCH2CCDMay 20, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.051
20.979051
30.951
ReflectionResolution: 1.37→20 Å / Num. all: 95653 / Num. obs: 94082 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.677 % / Biso Wilson estimate: 19.18 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 11.88
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.37-1.450.3973.9638261399194.7
1.45-1.550.2735.7680981438399.3
1.55-1.680.1868664171395799.5
1.68-1.830.13310.5552781160799.6
1.83-2.050.0914.1549621154299.8
2.05-2.360.06917.645723980799.6
2.36-2.880.06119.239108850099.6
2.88-4.030.0522.430191660898.8
4.03-50.04424.57950176994.5
5-100.03329.57803174692.7
10-200.0426.164717265.2
20

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.4.0062refinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.371→19.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.572 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4041 4.3 %RANDOM
Rwork0.187 ---
obs0.189 94023 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.399 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å20 Å2
2---0.73 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.371→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 55 480 4112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223700
X-RAY DIFFRACTIONr_angle_refined_deg1.262.0035015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3535454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99824.424165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38915645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2541521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212783
X-RAY DIFFRACTIONr_mcbond_it1.45522264
X-RAY DIFFRACTIONr_mcangle_it2.14533648
X-RAY DIFFRACTIONr_scbond_it1.63421436
X-RAY DIFFRACTIONr_scangle_it2.36331367
X-RAY DIFFRACTIONr_rigid_bond_restr1.32333700
X-RAY DIFFRACTIONr_sphericity_free4.5433484
X-RAY DIFFRACTIONr_sphericity_bonded4.51333623
LS refinement shellResolution: 1.371→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 277 -
Rwork0.244 6165 -
all-6442 -
obs--100 %

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