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Yorodumi- PDB-3u9x: Covalent attachment of pyridoxal-phosphate derivatives to 14-3-3 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u9x | ||||||
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Title | Covalent attachment of pyridoxal-phosphate derivatives to 14-3-3 proteins | ||||||
Components | 14-3-3 protein sigma | ||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / 14-3-3 / ADAPTER PROTEIN / PROTEIN-PROTEIN INTERACTION / N6-pyridoxal phosphate-L-lysine (PSI-MOD:128) / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Thiel, P. / Roeglin, L. / Kohlbacher, O. / Ottmann, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Covalent attachment of pyridoxal-phosphate derivatives to 14-3-3 proteins. Authors: Roglin, L. / Thiel, P. / Kohlbacher, O. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u9x.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u9x.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 3u9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/3u9x ftp://data.pdbj.org/pub/pdb/validation_reports/u9/3u9x | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 26729.982 Da / Num. of mol.: 1 / Fragment: UNP residues 1-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HME1, NM_006142, SFN / Plasmid: PPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: P31947 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.7 Å3/Da / Density % sol: 54.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.095M HEPES Na, 26.6% PEG400, 0.1M Calcium chloride, 5% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 8, 2011 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: curved multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→45.54 Å / Num. all: 26966 / Num. obs: 26966 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 22.755 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 35.76 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 28.82 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.54 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1836 / WRfactor Rwork: 0.1272 / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.903 / SU B: 3.97 / SU ML: 0.057 / SU R Cruickshank DPI: 0.2372 / SU Rfree: 0.1087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.16 Å2 / Biso mean: 17.6291 Å2 / Biso min: 3.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→45.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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