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- PDB-7dqr: Crystal structure of Sulfurisphaera tokodaii methylated O6-methyl... -

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Basic information

Entry
Database: PDB / ID: 7dqr
TitleCrystal structure of Sulfurisphaera tokodaii methylated O6-methylguanine methyltransferase
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: 1.74 Å
AuthorsKikuchi, M. / Yamauchi, T. / Iizuka, Y. / Tsonoda, 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. / Tsonoda, M.
History
DepositionDec 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 23, 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)18,0872
Polymers17,9911
Non-polymers961
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.206, 52.472, 61.775
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: 17990.979 Da / Num. of mol.: 1
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.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 43.03 %
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-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.74→48.21 Å / Num. obs: 16659 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.013 / Rrim(I) all: 0.034 / Net I/σ(I): 34.8 / Num. measured all: 107753 / Scaling rejects: 4
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
1.74-1.776.90.14263939260.9920.0580.15411.3100
8.87-48.214.50.0287141570.9990.0130.03153.698

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wrj

1wrj


Resolution: 1.74→39.992 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.196 / SU B: 2.022 / SU ML: 0.068 / Average fsc free: 0.9358 / Average fsc work: 0.9488 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2256 893 5.375 %
Rwork0.1887 15720 -
all0.191 --
obs-16613 99.862 %
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: 22.152 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20 Å20 Å2
2--0.002 Å2-0 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.74→39.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 5 100 1320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131255
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171223
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.6481693
X-RAY DIFFRACTIONr_angle_other_deg1.4751.5882823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.77621.38565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11215231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.255159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02293
X-RAY DIFFRACTIONr_nbd_refined0.2150.2228
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.21198
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2639
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2621
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.216
X-RAY DIFFRACTIONr_nbd_other0.2420.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.215
X-RAY DIFFRACTIONr_mcbond_it1.9792.033603
X-RAY DIFFRACTIONr_mcbond_other1.9752.028602
X-RAY DIFFRACTIONr_mcangle_it2.643.041753
X-RAY DIFFRACTIONr_mcangle_other2.6383.045754
X-RAY DIFFRACTIONr_scbond_it3.262.442652
X-RAY DIFFRACTIONr_scbond_other3.2372.435649
X-RAY DIFFRACTIONr_scangle_it4.9253.499938
X-RAY DIFFRACTIONr_scangle_other4.8943.487933
X-RAY DIFFRACTIONr_lrange_it5.62624.3091406
X-RAY DIFFRACTIONr_lrange_other5.63324.1411393
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
1.74-1.7850.24610.1911360.19311970.9270.9441000.171
1.785-1.8340.202590.19111070.19111670.9320.9499.91430.17
1.834-1.8870.288650.1910870.19511530.9220.94499.91330.173
1.887-1.9450.182540.17710600.17811160.9520.95499.82080.161
1.945-2.0090.204610.18110260.18210870.9450.9551000.172
2.009-2.0790.234490.1989770.19910280.9380.94499.80550.187
2.079-2.1570.187560.1969580.19510140.950.9441000.189
2.157-2.2450.268600.1879180.1929790.9060.94799.89790.183
2.245-2.3440.231520.1828750.1849280.9210.94999.89220.182
2.344-2.4580.28480.1738640.1789140.9280.95599.78120.176
2.458-2.5910.17320.1888170.1878490.9630.9541000.19
2.591-2.7470.218430.1997790.28230.9420.94399.87850.205
2.747-2.9360.279490.2167070.2217600.9050.92499.47370.232
2.936-3.170.237400.2096810.217210.9290.9411000.227
3.17-3.470.165370.1966300.1946670.9670.9551000.216
3.47-3.8760.198430.1675610.1696050.9580.96499.83470.189
3.876-4.4690.166300.1545200.1555510.9690.97199.81850.176
4.469-5.4560.288230.1844430.1874670.9160.9799.78590.215
5.456-7.6450.316180.223540.2243730.9450.95599.73190.246
7.645-39.9920.313130.2112200.2162370.9360.94998.31220.243

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