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- PDB-4wx9: Crystal structure of Mycobacterium tuberculosis OGT in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4wx9
TitleCrystal structure of Mycobacterium tuberculosis OGT in complex with DNA
Components
  • DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')
  • Methylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE / direct DNA damage reversal / alkylated DNA-protein alkyltransferase / protein-DNA complex
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
DNA / DNA (> 10) / Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMiggiano, R. / Rossi, F. / Garavaglia, S. / Rizzi, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
European CommunitySysteMTB HEALTH-F4-2010-241587 Italy
CitationJournal: Biochem.J. / Year: 2016
Title: Crystal structure of Mycobacterium tuberculosis O6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA.
Authors: Miggiano, R. / Perugino, G. / Ciaramella, M. / Serpe, M. / Rejman, D. / Pav, O. / Pohl, R. / Garavaglia, S. / Lahiri, S. / Rizzi, M. / Rossi, F.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3')
E: DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-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)61,6576
Polymers61,5655
Non-polymers921
Water1448
1
D: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3')
E: DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')
A: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules

C: Methylated-DNA--protein-cysteine methyltransferase

B: Methylated-DNA--protein-cysteine methyltransferase


Theoretical massNumber of molelcules
Total (without water)61,6576
Polymers61,5655
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
MethodPISA
2
B: Methylated-DNA--protein-cysteine methyltransferase

C: Methylated-DNA--protein-cysteine methyltransferase

D: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3')
E: DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')
A: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6576
Polymers61,5655
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_344-x-3/2,-y-1,z-1/21
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
MethodPISA
3
C: Methylated-DNA--protein-cysteine methyltransferase

B: Methylated-DNA--protein-cysteine methyltransferase

D: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3')
E: DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')
A: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6576
Polymers61,5655
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_345-x-3/2,-y-1,z+1/21
crystal symmetry operation3_445-x-1,y-1/2,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)43.481, 102.905, 137.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3')


Mass: 4020.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*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 / Source: (synth.) synthetic construct (others)
#3: Protein Methylated-DNA--protein-cysteine methyltransferase / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 17864.156 Da / Num. of mol.: 3 / Mutation: I2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ogt, Rv1316c, MTCY130.01c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WJW5, methylated-DNA-[protein]-cysteine S-methyltransferase
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M Ammonium acetate, 22% PEG 3350, 0.1M Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 3→82.3 Å / Num. obs: 12278 / % possible obs: 99.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.78
Reflection shellResolution: 3→3.16 Å / Redundancy: 5 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BHB, 1T39

4bhb

1t39


Resolution: 3→82.3 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 26.378 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.477 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26473 628 4.9 %RANDOM
Rwork0.19362 ---
obs0.19721 12278 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.49 Å2
Baniso -1Baniso -2Baniso -3
1--3.12 Å20 Å20 Å2
2--5.73 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 3→82.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 532 6 8 4271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0184408
X-RAY DIFFRACTIONr_bond_other_d0.0020.023927
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.8596092
X-RAY DIFFRACTIONr_angle_other_deg0.86339027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23922.959169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99415585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3041533
X-RAY DIFFRACTIONr_chiral_restr0.0690.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021013
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8255.671952
X-RAY DIFFRACTIONr_mcbond_other2.8255.6691951
X-RAY DIFFRACTIONr_mcangle_it4.5788.4992433
X-RAY DIFFRACTIONr_mcangle_other4.5788.52434
X-RAY DIFFRACTIONr_scbond_it3.4586.6132456
X-RAY DIFFRACTIONr_scbond_other3.4586.6132456
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6659.8363660
X-RAY DIFFRACTIONr_long_range_B_refined8.21852.9795208
X-RAY DIFFRACTIONr_long_range_B_other8.21752.9815209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 41 -
Rwork0.286 884 -
obs--99.89 %

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