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

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Basic information

Entry
Database: PDB / ID: 1zga
TitleCrystal structure of isoflavanone 4'-O-methyltransferase complexed with (+)-6a-hydroxymaackiain
ComponentsIsoflavanone 4'-O-methyltransferase'
KeywordsPlant Protein / Transferase / Rossmann 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-HMK / S-ADENOSYL-L-HOMOCYSTEINE / Isoflavone 4'-O-methyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 20, 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 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7803
Polymers40,0961
Non-polymers6852
Water2,468137
1
A: Isoflavanone 4'-O-methyltransferase'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)81,5616
Polymers80,1912
Non-polymers1,3694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_575x,-y+2,-z+1/21
Buried area10330 Å2
ΔGint-61 kcal/mol
Surface area30160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.217, 71.217, 188.907
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: 40095.652 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-HMK / (6AR,12AR)-6H-[1,3]DIOXOLO[5,6][1]BENZOFURO[3,2-C]CHROMENE-3,6A(12AH)-DIOL


Mass: 300.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O6
#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.: 137 / 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: 2.85 Å3/Da / Density % sol: 56.47 %
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: 0.97897 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2004 / Details: flat mirror
RadiationMonochromator: bent monochromator (horizontal focusing) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 21582 / Num. obs: 21559 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 18.8 Å2 / Rsym value: 0.117 / Net I/σ(I): 23.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 5 / Num. unique all: 2311 / Rsym value: 0.578 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→34.45 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 204856.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1987 9.9 %RANDOM
Rwork0.209 ---
all0.244 21545 --
obs0.209 20066 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.1587 Å2 / ksol: 0.319205 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-4 Å20 Å20 Å2
2--4 Å20 Å2
3----7.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.35→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2819 0 48 137 3004
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 315 10.2 %
Rwork0.245 2759 -
obs-2759 89.8 %
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 DIFFRACTION4hmk_mod3_xplo.paramhmk_mod3_xplo.top

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