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- PDB-1t38: HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAININ... -

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Basic information

Entry
Database: PDB / ID: 1t38
TitleHUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAINING O6-METHYLGUANINE
Components
  • 5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3'
  • 5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3'
  • Methylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE/DNA / ALKYLTRANSFERASE / METHYLTRANSFERASE / DNA REPAIR / HELIX-TURN-HELIX / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


MGMT-mediated DNA damage reversal / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA-methyltransferase activity / DNA alkylation repair / DNA ligation / positive regulation of double-strand break repair / methyltransferase activity / DNA repair / negative regulation of apoptotic process ...MGMT-mediated DNA damage reversal / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA-methyltransferase activity / DNA alkylation repair / DNA ligation / positive regulation of double-strand break repair / methyltransferase activity / DNA repair / negative regulation of apoptotic process / DNA binding / nucleoplasm / membrane / metal ion binding / nucleus
Similarity search - Function
Methylated DNA-protein cysteine methyltransferase domain / 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 / Double Stranded RNA Binding Domain ...Methylated DNA-protein cysteine methyltransferase domain / 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 / Double Stranded RNA 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDaniels, D.S. / Woo, T.T. / Luu, K.X. / Noll, D.M. / Clarke, N.D. / Pegg, A.E. / Tainer, J.A.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: DNA binding and nucleotide flipping by the human DNA repair protein AGT.
Authors: Daniels, D.S. / Woo, T.T. / Luu, K.X. / Noll, D.M. / Clarke, N.D. / Pegg, A.E. / Tainer, J.A.
#1: Journal: Embo J. / Year: 2000
Title: Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding
Authors: Daniels, D.S. / Mol, C.D. / Arvai, A.S. / Kanugula, S. / Pegg, A.E. / Tainer, J.A.
#2: Journal: Mutat.Res. / Year: 2000
Title: Conserved structural motifs governing the stoichiometric repair of alkylated DNA by O(6)-alkylguanine-DNA alkyltransferase
Authors: Daniels, D.S. / Tainer, J.A.
History
DepositionApr 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3'
C: 5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3'
A: Methylated-DNA--protein-cysteine methyltransferase


Theoretical massNumber of molelcules
Total (without water)28,2973
Polymers28,2973
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.698, 115.698, 106.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: DNA chain 5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3'


Mass: 4005.637 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3'


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Methylated-DNA--protein-cysteine methyltransferase / 6-O-methylguanine-DNA methyltransferase


Mass: 20339.408 Da / Num. of mol.: 1 / Mutation: C145S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGMT / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 3.17 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3000, Tris, sodium chloride, xylitol, calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 300011
2Tris11
3sodium chloride11
4xylitol11
5calcium acetate11
6H2O11
7PEG 300012
8sodium chloride12
9calcium acetate12
10H2O12

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→46 Å / Num. obs: 6205

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EH6

1eh6


Resolution: 3.2→29.32 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 4747888.28 / Data cutoff high rms absF: 4747888.28 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 343 5.5 %RANDOM
Rwork0.261 ---
all0.263 ---
obs0.261 6201 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.5433 Å2 / ksol: 0.206121 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a1.01 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 3.2→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 528 0 2 1697
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellHighest resolution: 3.2 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork974 -
Rfree-4.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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