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- PDB-6cig: CRYSTAL STRUCTURE ANALYSIS OF SELENOMETHIONINE SUBSTITUTED ISOFLA... -

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Basic information

Entry
Database: PDB / ID: 6cig
TitleCRYSTAL STRUCTURE ANALYSIS OF SELENOMETHIONINE SUBSTITUTED ISOFLAVONE O-METHYLTRANSFERASE
ComponentsIsoflavone-7-O-methyltransferase 8
KeywordsTRANSFERASE / selenomethionine / S-ADENOSYL-L-HOMOCYSTEINE 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
S-ADENOSYL-L-HOMOCYSTEINE / Chem-T3A / Isoflavone-7-O-methyltransferase 8
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsZubieta, C. / Dixon, R.A. / Shabalin, I.G. / Kowiel, M. / Porebski, P.J. / Noel, J.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
National Science Foundation (NSF, United States) United States
Citation
Journal: 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.
#1: Journal: Bioinformatics / Year: 2018
Title: Automatic Recognition of Ligands in Electron Density by Machine Learning.
Authors: Kowiel, M. / Brzezinski, D. / Porebski, P.J. / Shabalin, I.G. / Jaskolski, M. / Minor, W.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 7, 2018ID: 1FPX
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity / Item: _entity.formula_weight
Revision 1.2Dec 26, 2018Group: Data collection / Other / Structure summary
Category: audit_author / entity ...audit_author / entity / pdbx_SG_project / struct_keywords
Item: _entity.formula_weight / _struct_keywords.text
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoflavone-7-O-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4289
Polymers40,1341
Non-polymers1,2948
Water8,863492
1
A: Isoflavone-7-O-methyltransferase 8
hetero molecules

A: Isoflavone-7-O-methyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,85618
Polymers80,2672
Non-polymers2,58916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12250 Å2
ΔGint-109 kcal/mol
Surface area28930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.810, 50.240, 63.740
Angle α, β, γ (deg.)90.000, 106.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Isoflavone-7-O-methyltransferase 8 / 7-IOMT-8 / Isoflavone-O-methyltransferase 8


Mass: 40133.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Plasmid: PET15B / Production host: Escherichia coli (E. coli)
References: UniProt: O24529, isoflavone 7-O-methyltransferase

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Non-polymers , 6 types, 500 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-T3A / N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC ACID


Mass: 243.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO6S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: Protein in 25 mM HEPES (pH 7.5), 100 mM NaCl, 1 mM DTT was mixed at 1:1 ratio with the crystallization buffer 17% (w/v) PEG 8000, 0.05 M TAPS (pH 8.25), 0.35 M lithium sulfate, 2 mM DTT

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11051
21051
31051
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9746
SYNCHROTRONSSRL BL9-220.9785
SYNCHROTRONSSRL BL9-230.9787
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 12, 1999
ADSC QUANTUM 42CCDDec 12, 1999
ADSC QUANTUM 43CCDDec 12, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
3MADMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97461
20.97851
30.97871
ReflectionResolution: 1.65→99 Å / Num. obs: 52130 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 15.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Num. unique all: 4669 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→39.28 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.97 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0751 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.076
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 2622 5 %RANDOM
Rwork0.1461 ---
obs0.1475 49529 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 206.51 Å2 / Biso mean: 29.911 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.33 Å2
2--0.15 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.65→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 81 492 3319
Biso mean--39.63 40.24 -
Num. residues----349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192899
X-RAY DIFFRACTIONr_bond_other_d0.0020.022724
X-RAY DIFFRACTIONr_angle_refined_deg1.5852.0083921
X-RAY DIFFRACTIONr_angle_other_deg1.05936345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7045354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54125.041121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12115486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4791511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 167 -
Rwork0.224 3636 -
all-3803 -
obs--97.02 %
Refinement TLS params.Method: refined / Origin x: 6.796 Å / Origin y: 25.215 Å / Origin z: 15.605 Å
111213212223313233
T0.0622 Å2-0.003 Å20.0227 Å2-0.023 Å20.0044 Å2--0.0661 Å2
L0.7481 °20.0165 °20.3717 °2-0.1527 °20.0668 °2--0.6269 °2
S-0.0012 Å °-0.0171 Å °-0.0441 Å °0.0262 Å °-0.0105 Å °0.0004 Å °0.0201 Å °-0.01 Å °0.0117 Å °

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