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- PDB-1fp2: CRYSTAL STRUCTURE ANALYSIS OF ISOFLAVONE O-METHYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1fp2
TitleCRYSTAL STRUCTURE ANALYSIS OF ISOFLAVONE O-METHYLTRANSFERASE
ComponentsISOFLAVONE O-METHYLTRANSFERASE
KeywordsTRANSFERASE / protein-product complex
Function / homology
Function and homology information


isoflavone 7-O-methyltransferase / isoflavone 7-O-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'-HYDROXY-7-METHOXYISOFLAVONE / S-ADENOSYL-L-HOMOCYSTEINE / Isoflavone-7-O-methyltransferase 8
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsZubieta, C. / Dixon, R.A. / Noel, J.P.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases.
Authors: Zubieta, C. / He, X.Z. / Dixon, R.A. / Noel, J.P.
History
DepositionAug 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ISOFLAVONE O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3013
Polymers39,6491
Non-polymers6532
Water4,450247
1
A: ISOFLAVONE O-METHYLTRANSFERASE
hetero molecules

A: ISOFLAVONE O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6036
Polymers79,2972
Non-polymers1,3054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9750 Å2
ΔGint-82 kcal/mol
Surface area29030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)145.556, 50.538, 63.824
Angle α, β, γ (deg.)90.00, 106.69, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer constructed from chain A by a two-fold rotation.

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Components

#1: Protein ISOFLAVONE O-METHYLTRANSFERASE


Mass: 39648.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Production host: Escherichia coli (E. coli) / References: UniProt: O24529
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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-HMO / 4'-HYDROXY-7-METHOXYISOFLAVONE / ISOFORMONONETIN


Mass: 268.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: PEG 8000, lithium sulfate, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 15 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 %(w/v)PEG80001reservoir
20.05 MTAPS1reservoir
30.35 Mlithium sulfate1reservoir
42 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.4→99 Å / Num. all: 87599 / Num. obs: 82735 / % possible obs: 94.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 1.8 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.65 / Num. unique all: 6859 / % possible all: 65.5
Reflection
*PLUS
Num. measured all: 152679 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 65 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.3

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.4→69.71 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1360469.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 4162 5 %RANDOM
Rwork0.217 ---
all0.233 87599 --
obs0.217 82735 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.34 Å2 / ksol: 0.3714 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å2-0.45 Å2
2--3.8 Å20 Å2
3----1.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 1.4→69.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 46 247 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.022
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 583 4.8 %
Rwork0.37 11567 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SAH_PARA.TXTSAH_TOPO.TXT
X-RAY DIFFRACTION4ISOFORM_PARA.TXTISOFORM_TOPO.TXT
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.4
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.413 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.37

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