+Open data
-Basic information
Entry | Database: PDB / ID: 7c3q | ||||||
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Title | Human MdmX protein in complex with Nutlin3a | ||||||
Components | Protein Mdm4 | ||||||
Keywords | ONCOPROTEIN / MdmX / Nutlin-3a | ||||||
Function / homology | Function and homology information atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process / Regulation of TP53 Activity through Methylation / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / cellular response to hypoxia / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / protein stabilization / regulation of cell cycle / protein ubiquitination / Ub-specific processing proteases / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.801 Å | ||||||
Authors | Su, Z.D. / Cheng, X.Y. / Zhang, B.L. / Kuang, Z.K. / Yang, J. / Li, Z.C. / Yu, J.P. / Zhao, Z.T. / Cao, C.Z. | ||||||
Citation | Journal: To Be Published Title: Human MdmX protein in complex with Nutlin3a Authors: Su, Z.D. / Cheng, X.Y. / Zhang, B.L. / Kuang, Z.K. / Yang, J. / Li, Z.C. / Yu, J.P. / Zhao, Z.T. / Cao, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c3q.cif.gz | 54.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c3q.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 7c3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/7c3q ftp://data.pdbj.org/pub/pdb/validation_reports/c3/7c3q | HTTPS FTP |
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-Related 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: 11042.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O15151 |
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#2: Chemical | ChemComp-O4B / |
#3: Chemical | ChemComp-NUT / |
#4: Chemical | ChemComp-PEG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M HEPES sodium salt pH 7.5, 1.6 M Ammonium sulfate, 2%(w/v) PEG 1000 PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 3, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→42.433 Å / Num. obs: 10064 / % possible obs: 95.9 % / Redundancy: 23 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.015 / Rrim(I) all: 0.076 / Net I/σ(I): 25.4 | ||||||||||||||||||||||||||||||
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: 6Q9W, 6V4F Resolution: 1.801→42.433 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.134 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: 31.715 Å2
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Refinement step | Cycle: LAST / Resolution: 1.801→42.433 Å
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Refine LS restraints |
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LS refinement shell |
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