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- PDB-1eh7: METHYLATED HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1eh7
TitleMETHYLATED HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE
ComponentsO6-ALKYLGUANINE-DNA ALKYLTRANSFERASE
KeywordsTRANSFERASE / ALKYLTRANSFERASE / METHYLTRANSFERASE / DNA REPAIR
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
Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsDaniels, D.S. / Tainer, J.A.
CitationJournal: 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.
History
DepositionFeb 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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
A: O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7512
Polymers21,6861
Non-polymers651
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.401, 71.401, 76.325
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE / AGT / O6-METHYLGUANINE-DNA METHYLTRANSFERASE / MGMT


Mass: 21685.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: METHYLATED CYSTEINE 145 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18 MG/ML PROTEIN, 1.5 M SUCROSE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mg/mlprotein1drop
21.5 Msucrose1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 28548 / Num. obs: 15195 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 1.472 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.4926
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.858 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.133 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 28548
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: PDB 1EH6

1eh6


Resolution: 2→18.23 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1710146.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ILE 141 IS LOCATED IN A TIGHT TURN PRECEDING THE ACTIVE SITE AND CONSTRAINED IN A DISALLOWED RAMACHANDRAN REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1539 10.1 %RANDOM
Rwork0.199 ---
obs-22409 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.82 Å2 / ksol: 0.473 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-2.91 Å20 Å2
2---0.33 Å20 Å2
3---0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→18.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 1 182 1415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.551.5
X-RAY DIFFRACTIONc_mcangle_it12
X-RAY DIFFRACTIONc_scbond_it0.822
X-RAY DIFFRACTIONc_scangle_it1.22.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 250 9.8 %
Rwork0.242 2301 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ZN.PARAMZN.TOP
X-RAY DIFFRACTION4CYSM.PARAMCYSM.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / % reflection Rfree: 9.8 %

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