[English] 日本語
Yorodumi- PDB-8c57: CpG specific M.MpeI methyltransferase crystallized in the presenc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c57 | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CpG specific M.MpeI methyltransferase crystallized in the presence of 5,6-dihydro-5-azacytosine (converted to 5m-dhaC) and 5-methylcytosine containing dsDNA | |||||||||||||||||||||||||||
Components |
| |||||||||||||||||||||||||||
Keywords | TRANSFERASE / M.MpeI / DNA methyltransferase / DNA / 5-methylcytosine / 5-methyl-5 / 6-dihydro-5-azacytosine / 5mC / dhaC / CpG | |||||||||||||||||||||||||||
Function / homology | Function and homology information DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / methylation Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Malacoplasma penetrans HF-2 (bacteria) synthetic construct (others) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||||||||||||||||||||
Authors | Wojciechowski, M. / Czapinska, H. / Krwawicz, J. / Rafalski, D. / Bochtler, M. | |||||||||||||||||||||||||||
Funding support | Poland, European Union, 8items
| |||||||||||||||||||||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Cytosine analogues as DNA methyltransferase substrates. Authors: Wojciechowski, M. / Czapinska, H. / Krwawicz, J. / Rafalski, D. / Bochtler, M. #1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013 Title: CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI. Authors: Wojciechowski, M. / Czapinska, H. / Bochtler, M. #2: Journal: Science / Year: 2012 Title: Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. Authors: Song, J. / Teplova, M. / Ishibe-Murakami, S. / Patel, D.J. | |||||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8c57.cif.gz | 245.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8c57.ent.gz | 194.7 KB | Display | PDB format |
PDBx/mmJSON format | 8c57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c57_validation.pdf.gz | 786.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8c57_full_validation.pdf.gz | 788.1 KB | Display | |
Data in XML | 8c57_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 8c57_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c57 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c57 | HTTPS FTP |
-Related structure data
Related structure data | 8c56C 8c58C 8c59C 4dkjS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46238.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Malacoplasma penetrans HF-2 (bacteria) / Strain: HF-2 / Gene: MYPE4940 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): 2566 / References: UniProt: Q8EVR5 |
---|
-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4266.813 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
---|---|
#3: DNA chain | Mass: 4325.829 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Non-polymers , 4 types, 473 molecules
#4: Chemical | ChemComp-SAM / | ||
---|---|---|---|
#5: Chemical | ChemComp-CO3 / | ||
#6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 10% PEG 3350, 150 mM NaCl, 50 mM sodium citrate (final pH, 5.6). For cryoprotection glycerol was added to 25% v/v |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.2782 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2782 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 44130 / % possible obs: 95 % / Redundancy: 3.66 % / Biso Wilson estimate: 48.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.043 / Rsym value: 0.037 / Net I/σ(I): 18.27 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 3.58 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7029 / CC1/2: 0.685 / Rrim(I) all: 0.822 / Rsym value: 0.701 / % possible all: 96 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DKJ Resolution: 1.95→19.93 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 8.687 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED. SOLVENT MOLECULES HAVE BEEN MODELLED TENTATIVELY. S-ADENOSYLMETHIONINE (SAM) HAS BEEN MODELLED IN THE CO- ...Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED. SOLVENT MOLECULES HAVE BEEN MODELLED TENTATIVELY. S-ADENOSYLMETHIONINE (SAM) HAS BEEN MODELLED IN THE CO-SUBSTRATE BINDING POCKET BUT ONLY PARTS OF THE MOLECULE CORRESPONDING TO ITS BASE AND AMINO ACID END ARE RESOLVED IN THE ELECTRON DENSITY. THE CENTRAL PART OF THE CO-SUBSTRATE COULD NOT BE UNAMBIGUOUSLY TRACED, WHICH MAY BE DUE TO ITS DECOMPOSITION TO HOMOSERINE LACTONE (HSL) AND METHYLTHIOADENOSINE (MTA). 5,6-DIHYDRO-5-AZACYTOSINE CONTAINING DNA HAS BEEN USED FOR CRYSTALLIZATION BUT 5-METHYL-5,6-DIHYDRO-5-AZACYTOSINE IS OBSERVED IN THE CRYSTALS IN THE M.MPEI SUBSTRATE BINDING POCKET WHICH INDICATES THAT THE REACTION MUST HAVE TAKEN PLACE EITHER IN SOLUTION PRIOR TO CRYSTALLIZATION OR IN THE CRYSTAL. Since the pH of the crystallization drop (reservoir buffer pH 5.6) was close to the pK for the HCO3-/CO32-+H+ equilibrium (pKa=6.1), a mixture of carbonate and hydrogencarbonate is likely present in the crystal.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.612 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.95→19.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|