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- PDB-7dqt: Crystal structure of O6-methylguanine methyltransferase Y91F variant -

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Basic information

Entry
Database: PDB / ID: 7dqt
TitleCrystal structure of O6-methylguanine methyltransferase Y91F 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: 1.13 Å
AuthorsKikuchi, M. / Iizuka, Y. / Yamauchi, T. / 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

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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)18,1052
Polymers18,0091
Non-polymers961
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area8320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.102, 52.839, 61.837
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: 18008.951 Da / Num. of mol.: 1 / Mutation: Y91F
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.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v Pentaerythritol propoxylate (5/4 PO/OH)

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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 2M / Detector: PIXEL / Date: Nov 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→40.17 Å / Num. obs: 59665 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.069 / Net I/σ(I): 26.1 / Num. measured all: 755764 / 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
1.13-1.1511.70.1783324628450.9910.0530.18611.997.7
6.19-40.1711.10.07748354350.980.0250.08238.399.4

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Processing

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

1wrj


Resolution: 1.13→30.938 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.429 / SU ML: 0.021 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1966 2959 4.965 %
Rwork0.1712 56638 -
all0.172 --
obs-59597 99.826 %
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: 11.823 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20 Å20 Å2
2---0.001 Å20 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.13→30.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 5 208 1448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131402
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171366
X-RAY DIFFRACTIONr_angle_refined_deg2.1761.6531921
X-RAY DIFFRACTIONr_angle_other_deg1.571.583158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.41120.55672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5415256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.311511
X-RAY DIFFRACTIONr_chiral_restr0.1210.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021583
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02347
X-RAY DIFFRACTIONr_nbd_refined0.2250.2262
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21311
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2675
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.2678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2102
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3120.225
X-RAY DIFFRACTIONr_nbd_other0.2290.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.226
X-RAY DIFFRACTIONr_mcbond_it1.1791.026666
X-RAY DIFFRACTIONr_mcbond_other1.1781.025665
X-RAY DIFFRACTIONr_mcangle_it1.6641.549843
X-RAY DIFFRACTIONr_mcangle_other1.6631.551844
X-RAY DIFFRACTIONr_scbond_it1.9211.221736
X-RAY DIFFRACTIONr_scbond_other1.9221.22733
X-RAY DIFFRACTIONr_scangle_it2.7791.7541062
X-RAY DIFFRACTIONr_scangle_other2.7821.751056
X-RAY DIFFRACTIONr_lrange_it3.69213.0181623
X-RAY DIFFRACTIONr_lrange_other3.47912.2581568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.1590.2182210.194032X-RAY DIFFRACTION98.1764
1.159-1.1910.1852010.1924048X-RAY DIFFRACTION99.6015
1.191-1.2260.2042150.183925X-RAY DIFFRACTION99.9276
1.226-1.2630.2311790.1833846X-RAY DIFFRACTION100
1.263-1.3050.1892010.1843680X-RAY DIFFRACTION100
1.305-1.350.1921960.1723598X-RAY DIFFRACTION100
1.35-1.4010.1861870.1683454X-RAY DIFFRACTION100
1.401-1.4580.1621710.1653333X-RAY DIFFRACTION100
1.458-1.5230.2011600.1633198X-RAY DIFFRACTION100
1.523-1.5970.1921610.1623083X-RAY DIFFRACTION100
1.597-1.6840.1741440.152937X-RAY DIFFRACTION100
1.684-1.7860.1821260.1612806X-RAY DIFFRACTION100
1.786-1.9090.1991460.1672591X-RAY DIFFRACTION100
1.909-2.0610.1761550.1652412X-RAY DIFFRACTION100
2.061-2.2570.1981000.1572278X-RAY DIFFRACTION100
2.257-2.5230.191250.1582043X-RAY DIFFRACTION100
2.523-2.9110.216940.1781827X-RAY DIFFRACTION100
2.911-3.5610.212750.1731574X-RAY DIFFRACTION100
3.561-5.0160.188650.1621231X-RAY DIFFRACTION100
5.016-30.9380.249370.247742X-RAY DIFFRACTION99.3622

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