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- PDB-2qyo: Crystal structure of isoflavone O-methyltransferase homolog in co... -

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Basic information

Entry
Database: PDB / ID: 2qyo
TitleCrystal structure of isoflavone O-methyltransferase homolog in complex with biochanin A and SAH
ComponentsO-methyltransferase
KeywordsTRANSFERASE / isoflavone O-methyltransferase 3 / surface binding site
Function / homology
Function and homology information


isoflavone 7-O-methyltransferase / isoflavone 7-O-methyltransferase activity / : / S-adenosylmethionine-dependent 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-QSO / S-ADENOSYL-L-HOMOCYSTEINE / IOMT 3 / :
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, C. / Yu, X.-H. / Liu, C.-J.
CitationJournal: To be Published
Title: Crystal structures of Medicago truncatula isoflavone O-methyltransferase reveal conserved surface binding motifs critical for enzymatic activity
Authors: Wang, C. / Yu, X.-H. / Liu, C.-J.
History
DepositionAug 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-methyltransferase
B: O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,36319
Polymers80,5172
Non-polymers1,84617
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.540, 82.049, 101.034
Angle α, β, γ (deg.)90.00, 101.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein O-methyltransferase / / IOMT 3


Mass: 40258.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: Medicago truncatula IOMT3 gene / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q1SCE3, UniProt: Q06YR3*PLUS, isoflavone 4'-O-methyltransferase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-QSO / 5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one / Biochanin A / Biochanin A


Mass: 284.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5M potassium iodide, 40% PEG8000, 0.1M MOPSO, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 26, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 99681 / Num. obs: 51809 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.044 / Χ2: 1.108 / Net I/σ(I): 19.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.44 / Num. unique all: 5048 / Rsym value: 0.344 / Χ2: 0.739 / % possible all: 97.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Selenomethionine Protein

Resolution: 1.95→31.57 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4996 -RANDOM
Rwork0.214 ---
all-51886 --
obs-49464 95.5 %-
Displacement parametersBiso mean: 28.096 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å2-0.16 Å2
2---0.74 Å20 Å2
3----1.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.95→31.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 107 186 5869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.08
X-RAY DIFFRACTIONc_angle_deg0.15
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 1.95→2.04 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.297 557 -
Rwork0.251 --
obs-5569 86.3 %

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