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Yorodumi- PDB-4lg7: Crystal structure MBD4 MBD domain in complex with methylated CpG DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lg7 | ||||||
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Title | Crystal structure MBD4 MBD domain in complex with methylated CpG DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / Structural Genomics Consortium / SGC / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol ...satellite DNA binding / pyrimidine-specific mismatch base pair DNA N-glycosylase activity / depyrimidination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / DNA endonuclease activity / response to estradiol / nuclear speck / DNA repair / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Xu, C. / Tempel, W. / Wernimont, A.K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure MBD4 MBD domain in complex with methylated CpG DNA Authors: Xu, C. / Tempel, W. / Wernimont, A.K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lg7.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lg7.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lg7_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 4lg7_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 4lg7_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 4lg7_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/4lg7 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/4lg7 | HTTPS FTP |
-Related structure data
Related structure data | 3vxxS 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
#1: Protein | Mass: 7824.997 Da / Num. of mol.: 1 / Fragment: UNP residues 83-149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds | ||
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#2: DNA chain | Mass: 3677.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic #3: Chemical | ChemComp-UNX / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% PEG400, 5% MPD, 0.2 M sodium chloride, 0.1 M HEPES. protein:dna 1:1.2., pH 7.5, vapor diffusion, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 15, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→41.746 Å / Num. all: 5780 / Num. obs: 5780 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rsym value: 0.09 / Net I/σ(I): 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3VXX Resolution: 2.5→36 Å / Cor.coef. Fo:Fc: 0.9332 / Cor.coef. Fo:Fc free: 0.9179 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 Details: Refmac, phenix, coot, molprobity server were also used during refinement. We note the small number of reflections in the x-validation free set and a significant discrepancy between average ...Details: Refmac, phenix, coot, molprobity server were also used during refinement. We note the small number of reflections in the x-validation free set and a significant discrepancy between average refined and Wilson B-factors.
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Displacement parameters | Biso max: 112.01 Å2 / Biso mean: 57.9513 Å2 / Biso min: 29.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.53 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.79 Å / Total num. of bins used: 5
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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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