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Yorodumi- PDB-7kz1: Human MBD4 glycosylase domain bound to DNA containing an abasic site -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kz1 | ||||||
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Title | Human MBD4 glycosylase domain bound to DNA containing an abasic site | ||||||
Components |
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Keywords | HYDROLASE/DNA / protein-DNA complex / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å | ||||||
Authors | Pidugu, L.S. / Bright, H. / Pozharski, E. / Drohat, A.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Structural Insights into the Mechanism of Base Excision by MBD4. Authors: Pidugu, L.S. / Bright, H. / Lin, W.J. / Majumdar, C. / Van Ostrand, R.P. / David, S.S. / Pozharski, E. / Drohat, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kz1.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kz1.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 7kz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/7kz1 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/7kz1 | HTTPS FTP |
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-Related structure data
Related structure data | 7kz0C 7kzgC 4dk9S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18671.521 Da / Num. of mol.: 1 / Fragment: glycosylase domain (UNP residues 426-580) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MBD4, MED1 / Production host: Escherichia coli (E. coli) References: UniProt: O95243, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 3540.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3695.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 155 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-EDO / |
#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: 2.1 Å3/Da / Density % sol: 41.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG400, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.54 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2016 | |||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.62→37.61 Å / Num. obs: 28461 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.996 / Rpim(I) all: 0.058 / Net I/σ(I): 6.2 | |||||||||||||||||||||
Reflection shell |
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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 4DK9 Resolution: 1.62→37.61 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.52 Å2 / Biso mean: 37.2099 Å2 / Biso min: 12.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.62→37.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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