+Open data
-Basic information
Entry | Database: PDB / ID: 4dkj | ||||||
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Title | CpG specific methyltransferase in complex with target DNA | ||||||
Components |
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Keywords | TRANSFERASE/DNA / CG-SPECIFICITY / DNA INTERCALATION / CPG SEQUENCE / CYTOSINE C5-METHYLATION / C5-METHYLCYTOSINE / NUCLEOTIDE FLIPPING / S-adenosyl-L-methionine-dependent methyltransferases / C-5 cytosine-specific DNA methylases / DNA (cytosine-5-)-methyltransferase activity / DNA binding / DNA (cytosine-5-)-methylation / intracellular / TRANSFERASE-DNA complex | ||||||
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 | Mycoplasma penetrans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Wojciechowski, M. / Czapinska, H. / Bochtler, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI. Authors: Wojciechowski, M. / Czapinska, H. / Bochtler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dkj.cif.gz | 229.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dkj.ent.gz | 182.7 KB | Display | PDB format |
PDBx/mmJSON format | 4dkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dkj_validation.pdf.gz | 737.9 KB | Display | wwPDB validaton report |
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Full document | 4dkj_full_validation.pdf.gz | 740.5 KB | Display | |
Data in XML | 4dkj_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 4dkj_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/4dkj ftp://data.pdbj.org/pub/pdb/validation_reports/dk/4dkj | HTTPS FTP |
-Related structure data
Related structure data | 2c7pS S: Starting model for refinement |
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Similar structure data |
-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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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT CONTAINS PROTEIN CHAIN A, AND DNA STRANDS B AND C. THE TRIMER (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX OF THE MONOMERIC METHYLTRANSFERASE WITH ITS SUBSTRATE, DOUBLE STRANDED DNA. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 47310.082 Da / Num. of mol.: 1 / Mutation: S295P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma penetrans (bacteria) / Strain: HF-2 / Gene: MYPE4940 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 References: UniProt: Q8EVR5, DNA (cytosine-5-)-methyltransferase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4267.773 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 4325.829 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 269 molecules
#4: Chemical | ChemComp-SAH / |
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#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | AUTHORS STATE THAT THESE ARE NATURAL STRAIN VARIATIONS |
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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: 2.74 Å3/Da / Density % sol: 55.09 % |
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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. For cryoprotection glycerol was added to 25% v/v, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2010 / Details: BENT MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. all: 34324 / Num. obs: 34324 / % possible obs: 99.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4957 / Rsym value: 0.31 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2C7P Resolution: 2.15→38.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: (1) THE CRYSTAL WAS GROWN IN THE PRESENCE OF A SAMPLE THAT WAS LABELLED AS S-ADENOSYL-METHIONINE (SAM), BUT APPEARS TO HAVE BEEN DEGRADED TO S-ADENOSYL-HOMOCYSTEINE (SAH) EITHER PRIOR TO OR ...Details: (1) THE CRYSTAL WAS GROWN IN THE PRESENCE OF A SAMPLE THAT WAS LABELLED AS S-ADENOSYL-METHIONINE (SAM), BUT APPEARS TO HAVE BEEN DEGRADED TO S-ADENOSYL-HOMOCYSTEINE (SAH) EITHER PRIOR TO OR DURING CRYSTALLIZATION. PROGRAM CNS HAS BEEN USED FOR DNA REFINEMENT. NO SUGAR PUCKER CONSTRAINTS HAVE BEEN APPLIED. (2) THE MODELLED S-ADENOSYLHOMOCYSTEINE (SAH) IS UNCERTAIN. ITS BINDING SITE MIGHT BE OCCUPIED IN PART BY S-ADENOSYLMETHIONINE (SAM) OR THE SAM DEGRADATION PRODUCT 5 -METHYLTHIOADENOSINE (MTA) (FROM SCISSION OF SAM TO MTA AND HOMOSERINE LACTONE). THE DISTANCE BETWEEN CYS135 S AND C6 OF THE SUBSTRATE CYTOSINE BASE IS INTERMEDIATE BETWEEN A NON-COVALENT AND A COVALENT BOND. A DISTANCE BELOW THE VAN DER WAALS LIMIT SUGGESTS THAT SLIGHT DEVIATIONS FROM THE PLANARITY OF THE DNA BASE SHOULD OCCUR. AS THE RESOLUTION OF THE X-RAY DATA IS INSUFFICIENT TO DETECT SUCH DEVIATIONS, THEY WERE NOT MODELLED. (3) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→38.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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