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- PDB-1zhf: Crystal structure of selenomethionine substituted isoflavanone 4'... -

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Basic information

Entry
Database: PDB / ID: 1zhf
TitleCrystal structure of selenomethionine substituted isoflavanone 4'-O-methyltransferase
ComponentsIsoflavanone 4'-O-methyltransferase
KeywordsPlant Protein / Transferase / Isoflavanone 4'-O-methyltransferase / Rossmann fold
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
S-ADENOSYL-L-HOMOCYSTEINE / Isoflavone 4'-O-methyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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 25, 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)40,4802
Polymers40,0961
Non-polymers3841
Water1,56787
1
A: Isoflavanone 4'-O-methyltransferase
hetero molecules

A: Isoflavanone 4'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9604
Polymers80,1912
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_576x,-y+2,-z+3/21
Buried area8930 Å2
ΔGint-57 kcal/mol
Surface area31130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.355, 71.355, 188.800
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.93 Å3/Da / Density % sol: 57.7 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97932, 0.97942, 0.9855
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2004
Details: Mirror M1 Double crystal mono. Mirror M2 Distance from source 26m 81 29 m76 32m 71 Focusing type vert. foc. horiz. foc. by sagittal curved 2nd crystal vert. foc. Beam size at sample 0.3x0.3 ...Details: Mirror M1 Double crystal mono. Mirror M2 Distance from source 26m 81 29 m76 32m 71 Focusing type vert. foc. horiz. foc. by sagittal curved 2nd crystal vert. foc. Beam size at sample 0.3x0.3 mm2 Spectral range 8-25 keV Energy resolution 2 e-4 Flux at sample (at 1 A) .
RadiationMonochromator: At the Se K edge / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.979421
30.98551
ReflectionResolution: 2.5→80 Å / Num. all: 14700 / Num. obs: 19380 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.12 / Net I/σ(I): 7.46
Reflection shellResolution: 2.5→2.66 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→26.7 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2232073.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: As indicated by authors, after phasing, the SeMet residue was substituted by Met for subsequent refinement and therefore SeMet is not present in the coordinates
RfactorNum. reflection% reflectionSelection details
Rfree0.237 736 5 %RANDOM
Rwork0.204 ---
all0.243 17690 --
obs0.204 14700 83.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.6794 Å2 / ksol: 0.37381 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2--1.84 Å20 Å2
3----3.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.5→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2819 0 26 87 2932
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 87 4.8 %
Rwork0.231 1742 -
obs-1742 62.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2sah.paramsah.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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