+Open data
-Basic information
Entry | Database: PDB / ID: 3jzo | ||||||
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Title | Human MDMX liganded with a 12mer peptide (pDI) | ||||||
Components |
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Keywords | CELL CYCLE / P53-BINDING PROTEIN MDM4 / DOUBLE MINUTE 4 PROTEIN / Alternative splicing / Metal-binding / Nucleus / Polymorphism / Zinc / Zinc-finger | ||||||
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 / negative regulation of protein catabolic process / Stabilization of p53 / Oncogene Induced Senescence ...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 / negative regulation of protein catabolic process / Stabilization of p53 / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / Regulation of TP53 Degradation / ubiquitin-protein transferase activity / cellular response to hypoxia / protein-containing complex assembly / Regulation of TP53 Activity through Phosphorylation / Oxidative Stress Induced Senescence / protein stabilization / regulation of cell cycle / Ub-specific processing proteases / protein ubiquitination / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Schonbrunn, E. / Phan, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structure-based design of high affinity peptides inhibiting the interaction of p53 with MDM2 and MDMX. Authors: Phan, J. / Li, Z. / Kasprzak, A. / Li, B. / Sebti, S. / Guida, W. / Schonbrunn, E. / Chen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jzo.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jzo.ent.gz | 23.3 KB | Display | PDB format |
PDBx/mmJSON format | 3jzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jzo_validation.pdf.gz | 416.3 KB | Display | wwPDB validaton report |
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Full document | 3jzo_full_validation.pdf.gz | 416.3 KB | Display | |
Data in XML | 3jzo_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 3jzo_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/3jzo ftp://data.pdbj.org/pub/pdb/validation_reports/jz/3jzo | HTTPS FTP |
-Related structure data
Related structure data | 3jzpC 3jzqC 3jzrC 3jzsC 3dabS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 10160.899 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Plasmid: pDEST-His-MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) pLysS / References: UniProt: O15151 |
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#2: Protein/peptide | Mass: 1496.641 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-K / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.53 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 1.4 M Na/K phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 3, 2008 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 7677 / Num. obs: 7677 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 15.1 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3DAB Resolution: 1.8→25.35 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 413031.19 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→25.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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