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- PDB-7csm: Crystal structure of Sulfurisphaera tokodaii O6-methylguanine met... -

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Basic information

Entry
Database: PDB / ID: 7csm
TitleCrystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase C120S variant
ComponentsMethylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE / methyltransferase / Structural Genomics
Function / homology
Function and homology information


methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / methylation / cytoplasm
Similarity search - Function
Methylated-DNA--protein-cysteine methyltransferase / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKikuchi, M. / Yamauchi, T. / Iizuka, Y. / Tsunoda, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase.
Authors: Kikuchi, M. / Yamauchi, T. / Iizuka, Y. / Tsunoda, M.
History
DepositionAug 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0572
Polymers17,9611
Non-polymers961
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.213, 52.868, 62.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methylated-DNA--protein-cysteine methyltransferase / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 17960.887 Da / Num. of mol.: 1 / Mutation: C120S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: ogt, STK_09670 / Production host: Escherichia coli (E. coli)
References: UniProt: Q973C7, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→48.21 Å / Num. obs: 44164 / % possible obs: 99.1 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.016 / Rrim(I) all: 0.042 / Net I/σ(I): 27 / Num. measured all: 285375 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.25-1.276.50.181370721240.9840.0750.1959.397.9
6.85-48.215.80.03219123280.9990.0140.03548.399.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSMar 15, 2019data reduction
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRJ

1wrj


Resolution: 1.25→38.109 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.174 / SU B: 0.546 / SU ML: 0.025 / Average fsc free: 0.9562 / Average fsc work: 0.9614 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1924 2184 4.951 %
Rwork0.1688 41926 -
all0.17 --
obs-44110 98.879 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.221 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20 Å20 Å2
2---0 Å20 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.25→38.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 5 229 1477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131330
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171279
X-RAY DIFFRACTIONr_angle_refined_deg2.0951.6451808
X-RAY DIFFRACTIONr_angle_other_deg1.5381.5812973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7115171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.76821.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52315247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.873158
X-RAY DIFFRACTIONr_chiral_restr0.1250.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021471
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02297
X-RAY DIFFRACTIONr_nbd_refined0.2470.2291
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21241
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2672
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.2621
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3410.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.220
X-RAY DIFFRACTIONr_nbd_other0.1840.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4610.225
X-RAY DIFFRACTIONr_mcbond_it1.3361.154640
X-RAY DIFFRACTIONr_mcbond_other1.3281.152639
X-RAY DIFFRACTIONr_mcangle_it1.8341.735803
X-RAY DIFFRACTIONr_mcangle_other1.8331.738804
X-RAY DIFFRACTIONr_scbond_it2.2951.388690
X-RAY DIFFRACTIONr_scbond_other2.271.376684
X-RAY DIFFRACTIONr_scangle_it3.3461.987995
X-RAY DIFFRACTIONr_scangle_other3.3541.979989
X-RAY DIFFRACTIONr_lrange_it7.86515.9791631
X-RAY DIFFRACTIONr_lrange_other7.90215.1111553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.2211540.1842999X-RAY DIFFRACTION97.4351
1.282-1.3180.2091360.1782979X-RAY DIFFRACTION97.6795
1.318-1.3560.191500.1692862X-RAY DIFFRACTION97.7605
1.356-1.3970.1771450.1722782X-RAY DIFFRACTION98.2874
1.397-1.4430.1771520.1642708X-RAY DIFFRACTION98.5188
1.443-1.4940.1731550.1542648X-RAY DIFFRACTION98.7319
1.494-1.550.1521310.1522567X-RAY DIFFRACTION98.6833
1.55-1.6130.181360.1562439X-RAY DIFFRACTION98.9623
1.613-1.6850.21130.1552379X-RAY DIFFRACTION99.0855
1.685-1.7670.1721330.1552270X-RAY DIFFRACTION99.2155
1.767-1.8620.1711250.1612178X-RAY DIFFRACTION99.5677
1.862-1.9750.1681040.1592073X-RAY DIFFRACTION99.5883
1.975-2.1110.187970.1591950X-RAY DIFFRACTION99.6107
2.111-2.280.177890.1471819X-RAY DIFFRACTION99.7908
2.28-2.4960.208960.161682X-RAY DIFFRACTION99.9438
2.496-2.790.222690.1831551X-RAY DIFFRACTION99.8767
2.79-3.2190.178740.191362X-RAY DIFFRACTION100
3.219-3.9360.21640.1691176X-RAY DIFFRACTION100
3.936-5.540.23360.173940X-RAY DIFFRACTION99.8976
5.54-38.1090.227250.227562X-RAY DIFFRACTION99.3232

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