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- PDB-4bhc: CRYSTAL STRUCTURE OF THE M. TUBERCULOSIS O6-METHYLGUANINE METHYLT... -

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Basic information

Entry
Database: PDB / ID: 4bhc
TitleCRYSTAL STRUCTURE OF THE M. TUBERCULOSIS O6-METHYLGUANINE METHYLTRANSFERASE R37L VARIANT
ComponentsMETHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE
KeywordsTRANSFERASE / DNA REPAIR
Function / homology
Function and homology information


methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / response to nitrosative stress / DNA alkylation repair / methylation / plasma membrane / cytoplasm
Similarity search - Function
Methylated-DNA--protein-cysteine methyltransferase / 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 ...Methylated-DNA--protein-cysteine methyltransferase / 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 / Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsMiggiano, R. / Casazza, V. / Garavaglia, S. / Ciaramella, M. / Perugino, G. / Rizzi, M. / Rossi, F.
CitationJournal: J.Bacteriol. / Year: 2013
Title: Biochemical and Structural Studies on the M. Tuberculosis O6-Methylguanine Methyltransferase and Mutated Variants.
Authors: Miggiano, R. / Casazza, V. / Garavaglia, S. / Ciaramella, M. / Perugino, G. / Rizzi, M. / Rossi, F.
History
DepositionApr 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)17,8201
Polymers17,8201
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.116, 82.854, 37.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 17820.121 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A696, UniProt: P9WJW5*PLUS, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.5 Å3/Da / Density % sol: 52 % / Description: THE STARTING MODEL WAS THE WILD-TYPE STRUCTURE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 4572 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→33.926 Å / SU ML: 0.34 / σ(F): 1.36 / Phase error: 20.37 / Stereochemistry target values: LS_WUNIT_K1 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2227 30 0.4 %
Rwork0.1756 --
obs0.1757 4554 86.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 0 48 1304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091285
X-RAY DIFFRACTIONf_angle_d1.1171749
X-RAY DIFFRACTIONf_dihedral_angle_d14.993464
X-RAY DIFFRACTIONf_chiral_restr0.07195
X-RAY DIFFRACTIONf_plane_restr0.006230
LS refinement shellResolution: 2.8003→33.9285 Å
RfactorNum. reflection% reflection
Rfree0.2227 30 -
Rwork0.1756 7644 -
obs--87 %

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