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- PDB-4zyg: Crystal structure of methylated Sulfolobus solfataricus O6-methyl... -

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Basic information

Entry
Database: PDB / ID: 4zyg
TitleCrystal structure of methylated Sulfolobus solfataricus O6-methylguanine methyltransferase
ComponentsMethylated-DNA--protein-cysteine methyltransferase
KeywordsTRANSFERASE / extremophiles / DNA repair / alkylated DNA-protein alkyltransferase / methylated protein
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: 2.8 Å
AuthorsMiggiano, R. / Rossi, F. / Rizzi, M.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structure-function relationships governing activity and stability of a DNA alkylation damage repair thermostable protein.
Authors: Perugino, G. / Miggiano, R. / Serpe, M. / Vettone, A. / Valenti, A. / Lahiri, S. / Rossi, F. / Rossi, M. / Rizzi, M. / Ciaramella, M.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: 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 20, 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


Theoretical massNumber of molelcules
Total (without water)34,1482
Polymers34,1482
Non-polymers00
Water21612
1
A: Methylated-DNA--protein-cysteine methyltransferase


Theoretical massNumber of molelcules
Total (without water)17,0741
Polymers17,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methylated-DNA--protein-cysteine methyltransferase


Theoretical massNumber of molelcules
Total (without water)17,0741
Polymers17,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.486, 50.223, 142.026
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: 17074.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: ogt, SSO2487 / Plasmid: pQE31 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q97VW7, methylated-DNA-[protein]-cysteine S-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: Ammonium acetate 0.1 M, Bis-Tris 0.1 M pH 5.5, 17% PEG 17000
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.8→47.35 Å / Num. obs: 8764 / % possible obs: 97.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WRJ

1wrj


Resolution: 2.8→47.35 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2902 414 4.74 %
Rwork0.1909 --
obs0.1953 8729 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 0 12 2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092443
X-RAY DIFFRACTIONf_angle_d1.1943287
X-RAY DIFFRACTIONf_dihedral_angle_d14.866928
X-RAY DIFFRACTIONf_chiral_restr0.049363
X-RAY DIFFRACTIONf_plane_restr0.007411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-3.20530.34291410.24162740X-RAY DIFFRACTION98
3.2053-4.0380.31571300.18662764X-RAY DIFFRACTION97
4.038-47.35650.23831430.16912811X-RAY DIFFRACTION94

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