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- PDB-1yfh: wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Contai... -

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Basic information

Entry
Database: PDB / ID: 1yfh
Titlewt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Containing an Alkylated Cytosine
Components
  • 5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3'
  • 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-3'
  • Methylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE/DNA / protein-DNA complex / 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: 3.01 Å
AuthorsDuguid, E.M. / Rice, P.A. / He, C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The structure of the human AGT protein bound to DNA and its implications for damage detection.
Authors: Duguid, E.M. / Rice, P.A. / He, C.
History
DepositionDec 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-3'
E: 5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3'
F: 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-3'
G: 5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3'
A: Methylated-DNA--protein-cysteine methyltransferase
B: Methylated-DNA--protein-cysteine methyltransferase
C: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,69710
Polymers77,5017
Non-polymers1963
Water1086
1
D: 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-3'
E: 5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3'
C: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1994
Polymers29,1343
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-3'
G: 5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3'
A: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1994
Polymers29,1343
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2992
Polymers19,2331
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.150, 102.710, 87.940
Angle α, β, γ (deg.)90.00, 106.77, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe DNA bound to monomer B is completed by two fold axis -x +1, y +.5, -z +2.

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Components

#1: DNA chain 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-3'


Mass: 5144.413 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: oligonucleotide synthesized by automated phosphoramidite technique containing unatural base
#2: DNA chain 5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3'


Mass: 4756.123 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: oligonucleotide synthesized by automated phosphoramidite technique
#3: Protein Methylated-DNA--protein-cysteine methyltransferase / 2.1.1.63 / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 19233.285 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGMT / Plasmid: pGEX-6P-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.64 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PEG 4000, sodium chloride, citrate, magnesium chloride, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2sodium chloride11
3citrateCitric acid11
4magnesium chloride11
5H2O11
6PEG 400012
7sodium chloride12
8citrateCitric acid12
9magnesium chloride12

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2004 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: bent Ge (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 19770 / Num. obs: 19448 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.09 Å / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1T38

1t38


Resolution: 3.01→29.17 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 628363.49 / 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
Rfree0.286 835 4.8 %RANDOM
Rwork0.246 ---
all0.248 19769 --
obs0.246 17404 88 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.7255 Å2 / ksol: 0.311532 e/Å3
Displacement parametersBiso mean: 76.7 Å2
Baniso -1Baniso -2Baniso -3
1-13.14 Å20 Å219.18 Å2
2---33.9 Å20 Å2
3---20.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.92 Å0.85 Å
Refinement stepCycle: LAST / Resolution: 3.01→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 1316 3 6 4946
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 3.01→3.19 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.477 94 4.3 %
Rwork0.415 2101 -
obs--66.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3DNA_CSTAR.PARAMDNA_CSTAR.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP

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