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- PDB-1qnt: X-ray structure of human O6alkylguanine-DNA alkyltransferase -

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Basic information

Entry
Database: PDB / ID: 1qnt
TitleX-ray structure of human O6alkylguanine-DNA alkyltransferase
ComponentsMETHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE
KeywordsDNA REPAIR / ALKYLTRANSFERASE / METHYLTRANSFERASE
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 / positive regulation of double-strand break repair / methyltransferase activity / methylation / DNA repair ...MGMT-mediated DNA damage reversal / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA-methyltransferase activity / : / DNA alkylation repair / positive regulation of double-strand break repair / methyltransferase activity / methylation / DNA repair / negative regulation of apoptotic process / DNA binding / nucleoplasm / nucleus / membrane / metal ion binding
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
Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsWibley, J.E.A. / Moody, P.C.E.
Citation
Journal: Nucleic Acids Res. / Year: 2000
Title: Crystal Structure of the Human O(6)-Alkylguanine-DNA Alkyltransferase.
Authors: Wibley, J.E.A. / Pegg, A.E. / Moody, P.C.E.
#1: Journal: Embo J. / Year: 1994
Title: Crystal Structure of a Suicidal DNA Repair Protein: The Ada O6-Methylguanine-DNA Methyltransferase from E. Coli
Authors: Moore, M.H. / Gulbis, J.M. / Dodson, E.J. / Demple, B. / Moody, P.C.E.
#2: Journal: Anti-Cancer Drug Des. / Year: 1995
Title: A Homology Model of the 3-Dimensional Structure of Human O-6-Alklguanine-DNA Alkyltransferase Based on the Crystal Structure of the C-Terminal Domain of the Ada Protein from Escherichia Coli
Authors: Wibley J, J.E.A. / Mckie, H. / Embrey, K. / Marks, D.S. / Douglas, K.T. / Moore, M.H. / Moody, P.C.E.
History
DepositionOct 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)18,9501
Polymers18,9501
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.877, 71.877, 72.578
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsBIOLOGICAL_UNIT: MONOMER RECOMBINANT HUMAN PROTEINEXPRESSED IN ESCHERICHIA COLI

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Components

#1: Protein METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE / 6-O-METHYLGUANINE-DNA METHYLTRANSFERASE


Mass: 18949.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFRAGMENT EXPRESSED BY MUTATION OF POSITION 177 INTO A STOP CODON

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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: 2.86 Å3/Da / Density % sol: 55 %
Description: INITIAL STRUCTURE FROM MAD DATA COLLECTED TO 2.3A AT ESRF BM14 FROM SEMET DERIVATIVE USING DATA FROM 3 DIFFERENT WAVELENGTHS
Crystal growpH: 7.5 / Details: 1.75M (NH4)2SO4, PH 7.5
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMTris1drop
3200 mM1dropNaCl
410 mMdithiothreitol1drop
51.75 Mammonium sulfate1reservoir
6135 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→23 Å / Num. obs: 17402 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.05 / Net I/σ(I): 27.6
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 10.3 / Rsym value: 0.193 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 213536 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.193

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→23 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1600 4.9 %RANDOM
Rwork0.198 ---
obs0.198 32604 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.6075 Å2 / ksol: 0.427549 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20.71 Å20 Å2
2---0.55 Å20 Å2
3---1.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 0 174 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.137
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_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.561.5
X-RAY DIFFRACTIONc_mcangle_it12
X-RAY DIFFRACTIONc_scbond_it0.572
X-RAY DIFFRACTIONc_scangle_it0.942.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 250 4.8 %
Rwork0.22 5000 -
obs--95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.46
LS refinement shell
*PLUS
Rfactor Rwork: 0.22

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