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- PDB-1zgj: Crystal structure of isoflavanone 4'-O-methyltransferase complexe... -

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Basic information

Entry
Database: PDB / ID: 1zgj
TitleCrystal structure of isoflavanone 4'-O-methyltransferase complexed with (+)-pisatin
ComponentsIsoflavanone 4'-O-methyltransferase'
KeywordsPlant Protein / Transferase / Rossma fold / Isoflavanone 4'-O-methyltransferase
Function / homology
Function and homology information


2,7,4'-trihydroxyisoflavanone 4'-O-methyltransferase / isoflavone 4'-O-methyltransferase / isoflavone 4'-O-methyltransferase activity / 2,7,4'-trihydroxyisoflavanone-4'-O-methyltransferase activity / 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
Chem-P1S / S-ADENOSYL-L-HOMOCYSTEINE / Isoflavone 4'-O-methyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, C.-J. / Deavours, B.E. / Richard, S. / Ferrer, J.-L. / Dixon, R.A. / Noel, J.P.
CitationJournal: Plant Cell / Year: 2006
Title: Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses.
Authors: Liu, C.J. / Deavours, B.E. / Richard, S.B. / Ferrer, J.L. / Blount, J.W. / Huhman, D. / Dixon, R.A. / Noel, J.P.
History
DepositionApr 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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
Remark 999 SEQUENCE Currently there is no database reference available for Isoflavanone 4'-O- ... SEQUENCE Currently there is no database reference available for Isoflavanone 4'-O-methyltransferase, source Medicago truncatula

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoflavanone 4'-O-methyltransferase'
A: (6AR,12AR)-3-(HYDROXYMETHYL)-6H-[1,3]DIOXOLO[5,6][1]BENZOFURO[3,2-C]CHROMEN-6A(12AH)-OL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4493
Polymers39,7501
Non-polymers6992
Water41423
1
A: Isoflavanone 4'-O-methyltransferase'
hetero molecules

A: Isoflavanone 4'-O-methyltransferase'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8986
Polymers79,5012
Non-polymers1,3974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_575x,-y+2,-z+1/21
Buried area10530 Å2
ΔGint-63 kcal/mol
Surface area30010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.786, 71.786, 188.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Isoflavanone 4'-O-methyltransferase'


Mass: 39750.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Plasmid: pET28a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q29U70
#2: Chemical ChemComp-P1S / (6AR,12AR)-3-(HYDROXYMETHYL)-6H-[1,3]DIOXOLO[5,6][1]BENZOFURO[3,2-C]CHROMEN-6A(12AH)-OL / PISATIN


Mass: 314.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14O6
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277.16 K / Method: vapor diffusion / pH: 5.5
Details: PEG 8000, amonium acetate, DTT, pH 5.5, temperature 277.16K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2004 / Details: flat mirror
RadiationMonochromator: bent monochromator (horizontal focusing) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 17954 / Num. obs: 17937 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.138 / Net I/σ(I): 23.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 1745 / Rsym value: 0.533 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.5 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 242505.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1668 9.8 %RANDOM
Rwork0.234 ---
all0.238 17895 --
obs0.234 17018 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.2822 Å2 / ksol: 0.307738 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.62 Å20 Å20 Å2
2--1.03 Å20 Å2
3----5.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 49 23 2867
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 253 9.5 %
Rwork0.275 2401 -
obs-2654 90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2sah.paramsah.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4pisatin_o_xplo.parampisatin_o_xplo.top

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