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- PDB-6ga0: Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltran... -

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Basic information

Entry
Database: PDB / ID: 6ga0
TitleCrystal structure of a thermophilic O6-alkylguanine-DNA alkyltransferase-derived self-labeling protein-tag in covalent complex with SNAP-Vista Green
ComponentsMethylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE / O6-alkylguanine-DNA alkyltransferase / protein engineering / self-labeling protein tag / fluorescent probe / extremophiles
Function / homology
Function and homology information


methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / methylation / 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
Chem-ETW / Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiggiano, R. / Rossi, F. / Rizzi, M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of a thermophilic O6-alkylguanine-DNA alkyltransferase-derived self-labeling protein-tag in covalent complex with a fluorescent probe.
Authors: Rossi, F. / Morrone, C. / Massarotti, A. / Ferraris, D.M. / Valenti, A. / Perugino, G. / Miggiano, R.
History
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 23, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Jan 17, 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9144
Polymers19,2421
Non-polymers6723
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-19 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.779, 63.779, 159.038
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Methylated-DNA--protein-cysteine methyltransferase / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 19242.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The electron density map is not visible for the N-terminal His-tag and for five residues mapping at the C-terminal, that has been introduced in sub-cloning experiment.
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Gene: ogt, SSO2487 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97VW7, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Chemical ChemComp-ETW / 5-[(4-methylphenyl)methylcarbamoyl]-2-(6-oxidanyl-3-oxidanylidene-4~{H}-xanthen-9-yl)benzoic acid


Mass: 479.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H21NO6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2→79.52 Å / Num. obs: 13435 / % possible obs: 98.3 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.8
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.418 / Num. unique obs: 1296 / % possible all: 99.2

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Processing

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

4zye


Resolution: 2→79.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.607 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21899 692 5.2 %RANDOM
Rwork0.17557 ---
obs0.17776 12743 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.439 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å20 Å2
2---0.3 Å20 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 2→79.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 46 95 1361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191298
X-RAY DIFFRACTIONr_bond_other_d0.0010.021253
X-RAY DIFFRACTIONr_angle_refined_deg2.0312.041758
X-RAY DIFFRACTIONr_angle_other_deg0.9083.0012895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4062450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82315228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.29156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
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_it2.7982.843615
X-RAY DIFFRACTIONr_mcbond_other2.782.839614
X-RAY DIFFRACTIONr_mcangle_it3.8454.238767
X-RAY DIFFRACTIONr_mcangle_other3.8514.244768
X-RAY DIFFRACTIONr_scbond_it4.3063.203680
X-RAY DIFFRACTIONr_scbond_other3.9043.199674
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1034.621980
X-RAY DIFFRACTIONr_long_range_B_refined10.68123.9941591
X-RAY DIFFRACTIONr_long_range_B_other10.63923.7761563
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 59 -
Rwork0.209 905 -
obs--98.97 %

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