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- PDB-1fpq: CRYSTAL STRUCTURE ANALYSIS OF SELENOMETHIONINE SUBSTITUTED CHALCO... -

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Basic information

Entry
Database: PDB / ID: 1fpq
TitleCRYSTAL STRUCTURE ANALYSIS OF SELENOMETHIONINE SUBSTITUTED CHALCONE O-METHYLTRANSFERASE
ComponentsISOLIQUIRITIGENIN 2'-O-METHYLTRANSFERASE
KeywordsTRANSFERASE / selenomethionine substituted protein
Function / homology
Function and homology information


isoliquiritigenin 2'-O-methyltransferase / licodione 2'-O-methyltransferase / licodione 2'-O-methyltransferase activity / isoliquiritigenin 2'-O-methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / 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 / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / 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-ADENOSYLMETHIONINE / Isoliquiritigenin 2'-O-methyltransferase
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsZubieta, C. / Dixon, R.A. / Noel, J.P.
CitationJournal: 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.
History
DepositionAug 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISOLIQUIRITIGENIN 2'-O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2802
Polymers41,8821
Non-polymers3981
Water4,252236
1
A: ISOLIQUIRITIGENIN 2'-O-METHYLTRANSFERASE
hetero molecules

A: ISOLIQUIRITIGENIN 2'-O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5604
Polymers83,7632
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7860 Å2
ΔGint-82 kcal/mol
Surface area27210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.520, 53.470, 73.600
Angle α, β, γ (deg.)90.00, 124.62, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer formed by a twofold rotation of the monomer chain A.

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Components

#1: Protein ISOLIQUIRITIGENIN 2'-O-METHYLTRANSFERASE / CHALCONE O-METHYLTRANSFERASE


Mass: 41881.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Production host: Escherichia coli (E. coli) / References: UniProt: P93324
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, ammonium acetate, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %(w/v)PEG80001reservoir
20.05 MHEPES1reservoir
30.3 Mammonium acetate1reservoir
42 mMdithiothreitol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11051
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-210.929
SYNCHROTRONSSRL BL9-220.9795
SYNCHROTRONSSRL BL9-230.9797
SYNCHROTRONSSRL BL9-240.9793
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9291
20.97951
30.97971
40.97931
ReflectionResolution: 2→99 Å / Num. all: 27095 / Num. obs: 27095 / % possible obs: 98 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 6.9 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.205 / Num. unique all: 2143 / % possible all: 81
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 49336 / Num. measured all: 97770
Reflection shell
*PLUS
% possible obs: 81 % / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→32.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2347303.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
Details: F's are averaged from selenomethioine data collected at four wavelengths (SHARP output)
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1363 5.1 %RANDOM
Rwork0.247 ---
all0.295 27095 --
obs0.247 26958 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.81 Å2 / ksol: 0.3312 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å20 Å2-1.33 Å2
2--12.23 Å20 Å2
3----8.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 27 236 2833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.152
X-RAY DIFFRACTIONc_scangle_it1.732.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 198 4.6 %
Rwork0.304 4086 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3SAM_PARA.TXTSAM_TOPO.TXT
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.356 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.304

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