+Open data
-Basic information
Entry | Database: PDB / ID: 7ydt | ||||||
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Title | Crystal structure of mouse MPND | ||||||
Components | MPN domain containing protein | ||||||
Keywords | DNA BINDING PROTEIN / MPND | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases) / metallopeptidase activity / histone binding / transcription coactivator activity / chromatin remodeling / positive regulation of transcription by RNA polymerase II / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.055 Å | ||||||
Authors | Yang, M. / Chen, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structures of MPND Reveal the Molecular Recognition of Nucleosomes. Authors: Yang, M. / Li, X. / Tian, Z. / Ma, L. / Ma, J. / Liu, Y. / Shang, G. / Liang, A. / Wu, W. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ydt.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ydt.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ydt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/7ydt ftp://data.pdbj.org/pub/pdb/validation_reports/yd/7ydt | HTTPS FTP |
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-Related structure data
Related structure data | 7ydwC 6pbdS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17005.990 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mpnd / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TV65 #2: 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: 1.96 Å3/Da / Density % sol: 37.24 % / Description: slice |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Bis Tris, ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 17365 / % possible obs: 97.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.05→2.1 Å / Num. unique obs: 732 / CC1/2: 0.883 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PBD Resolution: 2.055→41.971 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.23 / SU B: 4.897 / SU ML: 0.126 / Average fsc free: 0.8886 / Average fsc work: 0.8981 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.16 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.645 Å2
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Refinement step | Cycle: LAST / Resolution: 2.055→41.971 Å
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Refine LS restraints |
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LS refinement shell |
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