+Open data
-Basic information
Entry | Database: PDB / ID: 6im9 | ||||||
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Title | MDM2 bound CueO-PM2 sensor | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Multicopper oxidase / Laccase / MDM2 | ||||||
Function / homology | Function and homology information cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / oxidoreductase activity, acting on metal ions / response to ether / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of signal transduction by p53 class mediator ...cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / oxidoreductase activity, acting on metal ions / response to ether / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / detoxification of copper ion / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / positive regulation of vascular associated smooth muscle cell migration / response to iron ion / peroxisome proliferator activated receptor binding / negative regulation of protein processing / response to copper ion / response to steroid hormone / NEDD8 ligase activity / SUMO transferase activity / AKT phosphorylates targets in the cytosol / cellular response to peptide hormone stimulus / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / blood vessel development / regulation of protein catabolic process / cardiac septum morphogenesis / Constitutive Signaling by AKT1 E17K in Cancer / ferroxidase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / ligase activity / protein sumoylation / SUMOylation of transcription factors / protein localization to nucleus / cellular response to actinomycin D / cellular response to UV-C / blood vessel remodeling / cellular response to estrogen stimulus / protein autoubiquitination / ribonucleoprotein complex binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of vascular associated smooth muscle cell proliferation / NPAS4 regulates expression of target genes / transcription repressor complex / regulation of heart rate / positive regulation of mitotic cell cycle / proteolysis involved in protein catabolic process / positive regulation of protein export from nucleus / response to cocaine / ubiquitin binding / Stabilization of p53 / Regulation of RUNX3 expression and activity / protein destabilization / cellular response to gamma radiation / RING-type E3 ubiquitin transferase / establishment of protein localization / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / response to toxic substance / cellular response to hydrogen peroxide / cellular response to growth factor stimulus / protein polyubiquitination / ubiquitin-protein transferase activity / endocytic vesicle membrane / ubiquitin protein ligase activity / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of TP53 Degradation / p53 binding / negative regulation of neuron projection development / outer membrane-bounded periplasmic space / 5S rRNA binding / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / periplasmic space / protein ubiquitination / regulation of cell cycle / Ub-specific processing proteases / response to xenobiotic stimulus / copper ion binding / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Wongsantichon, J. / Robinson, R. / Ghadessy, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Development and structural characterization of an engineered multi-copper oxidase reporter of protein-protein interactions. Authors: Sana, B. / Chee, S.M.Q. / Wongsantichon, J. / Raghavan, S. / Robinson, R.C. / Ghadessy, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6im9.cif.gz | 286.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6im9.ent.gz | 195.2 KB | Display | PDB format |
PDBx/mmJSON format | 6im9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/6im9 ftp://data.pdbj.org/pub/pdb/validation_reports/im/6im9 | HTTPS FTP |
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-Related structure data
Related structure data | 6im7C 6im8C 1kv7S 5wtsS 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
#1: Protein | Mass: 55846.766 Da / Num. of mol.: 1 / Mutation: M358I Source method: isolated from a genetically manipulated source Details: Chimera protein CueO-PM2 multicopper oxidase Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) synthetic construct (others) Strain: K12 / Gene: cueO, yacK, b0123, JW0119 / Production host: Escherichia coli (E. coli) / References: UniProt: P36649 |
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#2: Protein | Mass: 13749.694 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Production host: Escherichia coli (E. coli) References: UniProt: Q00987, RING-type E3 ubiquitin transferase |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.7 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 4M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→30 Å / Num. obs: 15209 / % possible obs: 98.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 66.85 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.023 / Rrim(I) all: 0.052 / Χ2: 0.902 / Net I/σ(I): 14.1 / Num. measured all: 77012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KV7 and 5WTS Resolution: 3.3→28.92 Å / SU ML: 0.4473 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.483 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 70.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→28.92 Å
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Refine LS restraints |
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LS refinement shell |
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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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