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

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Basic information

Entry
Database: PDB / ID: 7dqq
TitleCrystal structure of Sulfurisphaera tokodaii O6-methylguanine methyltransferase Y91F/C120S variant in complex with O6-methyldeoxyguanosine
ComponentsMethylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE / methyltramsferase
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/Winged helix DNA-binding domain ...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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-J03 / Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
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)18,2262
Polymers17,9451
Non-polymers2811
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint1 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.473, 53.166, 62.085
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-J03 / (2~{R},3~{S},5~{R})-5-(2-azanyl-6-methoxy-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol


Mass: 281.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5,000

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.47 Å / Num. obs: 5304 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Net I/σ(I): 32.3 / Num. measured all: 33206
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
2.6-2.726.60.13942256420.990.0590.15112.9100
9.01-48.475.20.01980815510.0090.02153.999.3

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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: 2.6→38.236 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.836 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.179 / SU B: 11.548 / SU ML: 0.247 / Average fsc free: 0.9099 / Average fsc work: 0.9365 / Cross valid method: FREE R-VALUE / ESU R Free: 0.379
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2841 265 5.025 %
Rwork0.1911 5009 -
all0.196 --
obs-5274 99.943 %
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: 27.542 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å20 Å20 Å2
2--0.042 Å2-0 Å2
3----0.039 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 20 41 1256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131270
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171214
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6711722
X-RAY DIFFRACTIONr_angle_other_deg1.2131.6012803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6845158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.00821.51566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.21615226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.534159
X-RAY DIFFRACTIONr_chiral_restr0.0710.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
X-RAY DIFFRACTIONr_nbd_refined0.2010.2247
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21088
X-RAY DIFFRACTIONr_nbtor_refined0.170.2611
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.240
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.212
X-RAY DIFFRACTIONr_nbd_other0.2110.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.213
X-RAY DIFFRACTIONr_mcbond_it2.0072.734605
X-RAY DIFFRACTIONr_mcbond_other2.0032.729604
X-RAY DIFFRACTIONr_mcangle_it3.3544.087757
X-RAY DIFFRACTIONr_mcangle_other3.3534.094758
X-RAY DIFFRACTIONr_scbond_it2.2623.089665
X-RAY DIFFRACTIONr_scbond_other2.263.093666
X-RAY DIFFRACTIONr_scangle_it3.7794.512960
X-RAY DIFFRACTIONr_scangle_other3.7774.517961
X-RAY DIFFRACTIONr_lrange_it6.33931.6461417
X-RAY DIFFRACTIONr_lrange_other6.33331.6931417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6670.389100.24382X-RAY DIFFRACTION100
2.667-2.740.363140.235344X-RAY DIFFRACTION100
2.74-2.8190.415150.214356X-RAY DIFFRACTION100
2.819-2.9060.287170.202318X-RAY DIFFRACTION100
2.906-30.311120.224332X-RAY DIFFRACTION100
3-3.1050.353180.2309X-RAY DIFFRACTION100
3.105-3.2220.295170.193304X-RAY DIFFRACTION100
3.222-3.3520.332230.191278X-RAY DIFFRACTION100
3.352-3.50.355160.183284X-RAY DIFFRACTION100
3.5-3.670.21460.2276X-RAY DIFFRACTION100
3.67-3.8660.218160.183253X-RAY DIFFRACTION99.6296
3.866-4.0990.253130.178251X-RAY DIFFRACTION100
4.099-4.3780.217130.153232X-RAY DIFFRACTION100
4.378-4.7240.138140.134209X-RAY DIFFRACTION100
4.724-5.1680.294140.18200X-RAY DIFFRACTION100
5.168-5.7670.23190.194186X-RAY DIFFRACTION100
5.767-6.6360.29970.166169X-RAY DIFFRACTION100
6.636-8.0730.269130.183140X-RAY DIFFRACTION100
8.073-11.1960.193100.163112X-RAY DIFFRACTION99.187
11.196-38.2360.55880.33474X-RAY DIFFRACTION98.7952

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