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- PDB-5llq: Crystal structure of Sulfolobus solfataricus O6-methylguanine met... -

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Basic information

Entry
Database: PDB / ID: 5llq
TitleCrystal structure of Sulfolobus solfataricus O6-methylguanine methyltransferase C119F variant
ComponentsMethylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE / DNA dealkylation / OGT / inactive mutant
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
Methylated-DNA--protein-cysteine methyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMiggiano, R. / Rossi, F. / Rizzi, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Interdomain interactions rearrangements control the reaction steps of a thermostable DNA alkyltransferase.
Authors: Morrone, C. / Miggiano, R. / Serpe, M. / Massarotti, A. / Valenti, A. / Del Monaco, G. / Rossi, M. / Rossi, F. / Rizzi, M. / Perugino, G. / Ciaramella, M.
History
DepositionJul 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jan 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,5424
Polymers37,3582
Non-polymers1842
Water54030
1
A: Methylated-DNA--protein-cysteine methyltransferase


Theoretical massNumber of molelcules
Total (without water)18,6791
Polymers18,6791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8633
Polymers18,6791
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.859, 85.850, 98.480
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: Protein Methylated-DNA--protein-cysteine methyltransferase / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 18678.805 Da / Num. of mol.: 2
Mutation: Catalytic Cysteine 119 is substituted by Phenilalanine
Source method: isolated from a genetically manipulated source
Details: Residues belonging to His-tag were not visible in the electron density. For this reason they were removed from coordinates file.
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Gene: ogt, SSO2487 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q97VW7, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.94 Å3/Da / Density % sol: 58.19 % / Description: Thin needle
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0,2 M ammonium phosphate monobasic 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.7→49.24 Å / Num. obs: 12411 / % possible obs: 96.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.26
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.35 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZYE

4zye


Resolution: 2.7→49.24 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23
RfactorNum. reflection% reflection
Rfree0.2368 640 5.16 %
Rwork0.1725 --
obs0.1761 12406 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 12 30 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082447
X-RAY DIFFRACTIONf_angle_d1.1373289
X-RAY DIFFRACTIONf_dihedral_angle_d14.358929
X-RAY DIFFRACTIONf_chiral_restr0.039360
X-RAY DIFFRACTIONf_plane_restr0.005411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.90840.27921230.21812325X-RAY DIFFRACTION97
2.9084-3.20110.28011260.20782301X-RAY DIFFRACTION96
3.2011-3.66420.2661220.17332326X-RAY DIFFRACTION97
3.6642-4.61590.20851470.14122336X-RAY DIFFRACTION96
4.6159-49.2480.21581220.17112478X-RAY DIFFRACTION96

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