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Yorodumi- PDB-3vxx: Crystal structure of methyl CpG binding domain of MBD4 in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vxx | ||||||
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Title | Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/5mCG sequence | ||||||
Components |
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Keywords | HYDROLASE/DNA / methyl CpG binding domain / protein-DNA complex / versatile base recognition / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / DNA repair / DNA damage response / chromatin ...Cleavage of the damaged pyrimidine / Displacement of DNA glycosylase by APEX1 / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / mitotic G2 DNA damage checkpoint signaling / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / DNA repair / DNA damage response / chromatin / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å | ||||||
Authors | Otani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Ariyoshi, M. / Shirakawa, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4 Authors: Otani, J. / Arita, K. / Kato, T. / Kinoshita, M. / Kimura, H. / Suetake, I. / Tajima, S. / Ariyoshi, M. / Shirakawa, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vxx.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vxx.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 3vxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vxx_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 3vxx_full_validation.pdf.gz | 463.8 KB | Display | |
Data in XML | 3vxx_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 3vxx_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/3vxx ftp://data.pdbj.org/pub/pdb/validation_reports/vx/3vxx | HTTPS FTP |
-Related structure data
Related structure data | 3vxvSC 3vybC 3vyqC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 7829.089 Da / Num. of mol.: 1 / Fragment: methyl CpG binding domain, UNP residues 69-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mbd4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9Z2D7, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4263.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis |
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#3: DNA chain | Mass: 4325.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis |
-Non-polymers , 3 types, 132 molecules
#4: Chemical | ChemComp-ACT / #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 3.53 Å3/Da / Density % sol: 65.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 7% PEG 10000, 0.1M sodium acetate, 0.2M sodium chloride, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 12096 / Num. obs: 12048 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 41.31 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VXV Resolution: 2.204→28.339 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.734 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.83 Å2 / Biso min: 20.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.204→28.339 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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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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