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- PDB-6iwt: Crystal structure of methyltransferase COMT-S in P. praeruptorum -

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Basic information

Entry
Database: PDB / ID: 6iwt
TitleCrystal structure of methyltransferase COMT-S in P. praeruptorum
ComponentsPmethyltransferase pCOMT-S
KeywordsTRANSFERASE / O-methyltransferase / O-methylation / evolution
Function / homology
Function and homology information


: / : / catechol O-methyltransferase activity / catechol O-methyltransferase / 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
DI(HYDROXYETHYL)ETHER / Caffeic acid O-methyltransferase-like protein
Similarity search - Component
Biological speciesPeucedanum praeruptorum (bai hua qian hu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsWang, N.N. / Zeng, Z.X.
CitationJournal: Int J Mol Sci / Year: 2019
Title: The Molecular and Structural Basis ofO-methylation Reaction in Coumarin Biosynthesis inPeucedanum praeruptorumDunn.
Authors: Zhao, Y. / Wang, N. / Sui, Z. / Huang, C. / Zeng, Z. / Kong, L.
History
DepositionDec 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pmethyltransferase pCOMT-S
B: Pmethyltransferase pCOMT-S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2574
Polymers80,0452
Non-polymers2122
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-70 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.370, 70.390, 59.650
Angle α, β, γ (deg.)90.000, 97.870, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 17 - 362 / Label seq-ID: 17 - 362

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Pmethyltransferase pCOMT-S


Mass: 40022.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peucedanum praeruptorum (bai hua qian hu)
Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A4P8DY91*PLUS
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MES monohydrate pH 6.0, 22% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.53→66.59 Å / Num. obs: 27497 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 74.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Net I/σ(I): 14.9
Reflection shellResolution: 2.53→2.62 Å / Rmerge(I) obs: 0.586 / Num. unique obs: 7085 / CC1/2: 0.735 / Rpim(I) all: 0.372

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11_2567refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KYZ

1kyz


Resolution: 2.53→66.589 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.44
RfactorNum. reflection% reflection
Rfree0.2614 1391 5.06 %
Rwork0.1886 --
obs0.1923 27488 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.67 Å2 / Biso mean: 82.536 Å2 / Biso min: 36.79 Å2
Refinement stepCycle: final / Resolution: 2.53→66.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 14 4 5322
Biso mean--74.54 60.63 -
Num. residues----692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085444
X-RAY DIFFRACTIONf_angle_d1.0717362
X-RAY DIFFRACTIONf_chiral_restr0.059824
X-RAY DIFFRACTIONf_plane_restr0.008938
X-RAY DIFFRACTIONf_dihedral_angle_d12.6663282
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3142X-RAY DIFFRACTION14.835TORSIONAL
12B3142X-RAY DIFFRACTION14.835TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5301-2.62050.34791460.2996263298
2.6205-2.72540.35741310.2971252093
2.7254-2.84950.33511460.2843256595
2.8495-2.99970.32731250.2445263297
2.9997-3.18760.31341320.2269271199
3.1876-3.43380.32791650.228259097
3.4338-3.77930.27741400.2032256295
3.7793-4.32610.22981380.1756253493
4.3261-5.450.24921340.1599267597
5.45-100.21061340.1537267695
Refinement TLS params.Method: refined / Origin x: 65.2208 Å / Origin y: -2.2881 Å / Origin z: 56.1644 Å
111213212223313233
T0.5564 Å2-0.0074 Å20.0081 Å2-0.3984 Å2-0.141 Å2--0.3417 Å2
L3.1312 °2-0.8853 °20.2843 °2-1.6947 °2-0.8435 °2--1.4846 °2
S0.2499 Å °0.1201 Å °0.0643 Å °-0.0767 Å °-0.2096 Å °-0.0101 Å °-0.034 Å °0.2597 Å °-0.032 Å °
Refinement TLS groupSelection details: all

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