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- PDB-7d4v: Crystal structure of Sulfurisphaera tokodaii O6-methylguanine met... -

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Basic information

Entry
Database: PDB / ID: 7d4v
TitleCrystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase Y91F/C120S variant
ComponentsMethylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE / methyltransferase
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: 1.78 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
DepositionSep 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation
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 1.3Oct 30, 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)18,0412
Polymers17,9451
Non-polymers961
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.848, 52.056, 62.336
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: 17944.887 Da / Num. of mol.: 1 / Mutation: Y91F, 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.: 55 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
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 3, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→47.85 Å / Num. obs: 15471 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.013 / Rrim(I) all: 0.034 / Net I/σ(I): 33.3 / Num. measured all: 98283 / 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
1.78-1.826.50.1656258670.9860.0670.1749.5100
9.08-47.855.10.0237631500.9990.010.02552.499.3

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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: 1.78→39.956 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.221 / SU B: 3.264 / SU ML: 0.103 / Average fsc free: 0.9031 / Average fsc work: 0.9197 / Cross valid method: FREE R-VALUE / ESU R: 0.134 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2452 656 4.252 %
Rwork0.2064 14771 -
all0.208 --
obs-15427 99.754 %
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: 27.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.022 Å20 Å2-0 Å2
2--0.003 Å20 Å2
3---0.019 Å2
Refinement stepCycle: LAST / Resolution: 1.78→39.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 5 55 1246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131225
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171158
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.6431656
X-RAY DIFFRACTIONr_angle_other_deg1.4211.5782674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.02821.86459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42415209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.786157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021353
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02272
X-RAY DIFFRACTIONr_nbd_refined0.2120.2223
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.21083
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2617
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.239
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.211
X-RAY DIFFRACTIONr_nbd_other0.2070.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4080.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.4140.22
X-RAY DIFFRACTIONr_mcbond_it2.8372.78603
X-RAY DIFFRACTIONr_mcbond_other2.7782.778602
X-RAY DIFFRACTIONr_mcangle_it3.5314.156753
X-RAY DIFFRACTIONr_mcangle_other3.5314.159754
X-RAY DIFFRACTIONr_scbond_it3.3173.124622
X-RAY DIFFRACTIONr_scbond_other3.2753.101619
X-RAY DIFFRACTIONr_scangle_it4.8314.542901
X-RAY DIFFRACTIONr_scangle_other4.774.507896
X-RAY DIFFRACTIONr_lrange_it5.97632.4741342
X-RAY DIFFRACTIONr_lrange_other5.9832.3961335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.78-1.8260.275610.21710440.2211050.9260.9431000.193
1.826-1.8760.285440.25210610.25311050.8910.8861000.213
1.876-1.9310.317410.2510270.25310680.8560.8711000.222
1.931-1.990.349440.2389770.24310210.8540.8951000.214
1.99-2.0550.306430.2289610.23210040.8880.9081000.208
2.055-2.1270.299340.2279340.2299690.8780.91499.89680.211
2.127-2.2070.269470.2279010.2299480.8830.9091000.216
2.207-2.2970.279470.2298590.2329060.9050.9111000.223
2.297-2.3990.294390.2138250.2178650.8920.92899.88440.214
2.399-2.5150.234430.2167900.2178410.9310.92699.04880.216
2.515-2.6510.28310.2097590.2127920.8980.92599.74750.215
2.651-2.8110.283230.2177470.2197720.8820.92299.74090.228
2.811-3.0040.226170.2296890.2297080.9060.91799.71750.246
3.004-3.2430.244360.2296230.236650.9110.92199.09770.245
3.243-3.550.251260.2025870.2046160.9180.94199.5130.23
3.55-3.9650.202240.1745440.1765710.9540.9699.47460.203
3.965-4.5710.213180.1594780.1615000.9670.97299.20.195
4.571-5.580.211120.1744220.1754360.970.96799.54130.208
5.58-7.8160.156130.1973380.1953540.9680.96199.15250.242
7.816-39.9560.179130.212050.2092190.960.96199.54340.263

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