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

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Basic information

Entry
Database: PDB / ID: 7dkn
TitleCrystal structure of Sulfurisphaera tokodaii 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: 1.79 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
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 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 1.3Nov 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)18,1693
Polymers17,9771
Non-polymers1922
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.072, 52.705, 61.618
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: 17976.953 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
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: 1.79→40.052 Å / Num. obs: 15203 / % possible obs: 99.3 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Net I/σ(I): 20.8
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
1.79-1.833.30.14126968150.9730.0850.1666.292.4
8.95-40.0550.0327581530.9990.0140.03630.799.3

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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: 1.79→40.052 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.514 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.128 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2192 726 4.788 %
Rwork0.1802 14438 -
all0.182 --
obs-15164 99.079 %
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: 17.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.018 Å20 Å2
3---0.008 Å2
Refinement stepCycle: LAST / Resolution: 1.79→40.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 10 106 1323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131291
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171260
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.651752
X-RAY DIFFRACTIONr_angle_other_deg1.4141.5882918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3835165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.68421.51566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99815241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.079159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021423
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
X-RAY DIFFRACTIONr_nbd_refined0.2090.2237
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.21200
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2637
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2593
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.267
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.214
X-RAY DIFFRACTIONr_nbd_other0.1910.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.40.219
X-RAY DIFFRACTIONr_mcbond_it1.6321.623615
X-RAY DIFFRACTIONr_mcbond_other1.5831.619614
X-RAY DIFFRACTIONr_mcangle_it2.3562.424771
X-RAY DIFFRACTIONr_mcangle_other2.3552.429772
X-RAY DIFFRACTIONr_scbond_it2.3461.965676
X-RAY DIFFRACTIONr_scbond_other2.2721.926669
X-RAY DIFFRACTIONr_scangle_it3.6752.819973
X-RAY DIFFRACTIONr_scangle_other3.6012.754962
X-RAY DIFFRACTIONr_lrange_it5.33919.3191447
X-RAY DIFFRACTIONr_lrange_other5.30119.2031436
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
1.79-1.8360.183470.189760.1811070.9530.9492.41190.165
1.836-1.8870.3510.1949980.19910890.8930.92696.32690.181
1.887-1.9410.215490.1939910.19510420.9340.93799.80810.181
1.941-2.0010.252560.199770.19410340.9190.93899.90330.182
2.001-2.0660.244600.1969190.1999810.9180.92899.79610.187
2.066-2.1390.208360.199220.1919590.9490.9499.89570.186
2.139-2.2190.237450.1788840.1819300.9330.95199.89250.177
2.219-2.3090.211400.1668610.1689010.9520.9561000.167
2.309-2.4120.152420.1628190.1618610.9550.9591000.164
2.412-2.5290.221340.187990.1828330.9560.9541000.185
2.529-2.6650.212380.1867420.1877810.9460.9599.8720.191
2.665-2.8260.237360.1837150.1857510.9370.9441000.192
2.826-3.020.259300.196740.1937050.9250.93799.85820.205
3.02-3.2610.278270.1946450.1976750.9220.94799.55560.212
3.261-3.5690.205280.1715750.1736040.9510.96299.83440.192
3.569-3.9870.206210.1525290.1545530.9620.97199.45750.174
3.987-4.5960.138280.1444760.1445040.9780.9781000.168
4.596-5.610.264250.1814040.1864290.9490.9681000.212
5.61-7.8580.201180.2123320.2123500.9510.9561000.249
7.858-40.0520.238150.2352000.2352160.960.94999.5370.275

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