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Yorodumi- PDB-8c56: CpG specific M.MpeI methyltransferase crystallized in the presenc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c56 | |||||||||||||||||||||||||||
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Title | CpG specific M.MpeI methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mZ) and 5-methylcytosine containing dsDNA | |||||||||||||||||||||||||||
Components |
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Keywords | TRANSFERASE / M.MpeI / DNA methyltransferase / DNA / 5-methylcytosine / 5-methyl-zebularine / 5mZ / 5mZeb / 5mC / 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: 2.4 Å | |||||||||||||||||||||||||||
Authors | Wojciechowski, M. / Czapinska, H. / Krwawicz, J. / Rafalski, D. / Bochtler, M. | |||||||||||||||||||||||||||
Funding support | Poland, European Union, 8items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c56.cif.gz | 239.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c56.ent.gz | 189.4 KB | Display | PDB format |
PDBx/mmJSON format | 8c56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c56_validation.pdf.gz | 774.7 KB | Display | wwPDB validaton report |
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Full document | 8c56_full_validation.pdf.gz | 777.1 KB | Display | |
Data in XML | 8c56_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 8c56_validation.cif.gz | 33.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c56 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c56 | HTTPS FTP |
-Related structure data
Related structure data | 8c57C 8c58C 8c59C 4dkjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-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 |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4248.794 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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#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, 415 molecules
#4: Chemical | ChemComp-SAH / |
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#5: Chemical | ChemComp-GOL / |
#6: Chemical | ChemComp-NA / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.16 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 25251 / % possible obs: 99.6 % / Redundancy: 8.6 % / Biso Wilson estimate: 53.298 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.121 / Rsym value: 0.114 / Net I/σ(I): 16.89 |
Reflection shell | Resolution: 2.4→2.54 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 3914 / CC1/2: 0.703 / Rrim(I) all: 1.277 / Rsym value: 1.203 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DKJ Resolution: 2.4→19.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 20.142 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED. IONS AND SOLVENT MOLECULES HAVE BEEN MODELLED TENTATIVELY. S-ADENOSYLHOMOCYSTEINE (SAH) HAS BEEN MODELLED ...Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED. IONS AND SOLVENT MOLECULES HAVE BEEN MODELLED TENTATIVELY. S-ADENOSYLHOMOCYSTEINE (SAH) 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-PRODUCT COULD NOT BE UNAMBIGUOUSLY TRACED, WHICH MAY BE DUE TO THE DECOMPOSITION OF THE CO-SUBSTRATE S-ADENOSYLMETHIONINE (SAM) USED FOR CRYSTALLIZATION TO HOMOSERINE LACTONE (HSL) AND METHYLTHIOADENOSINE (MTA). THE DISTANCE BETWEEN THE CATALYTIC CYSTEINE (CYS135) OF THE PROTEIN AND THE C6 ATOM OF THE SUBSTRATE BASE IS BETWEEN A COVALENT AND NON-COVALENT BOND AND HAS NOT BEEN CONSTRAINED DURING THE REFINEMENT.
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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: 51.84 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→19.89 Å
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Refine LS restraints |
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