+Open data
-Basic information
Entry | Database: PDB / ID: 4i7c | ||||||
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Title | Siah1 mutant bound to synthetic peptide (ACE)KLRPV(23P)MVRPWVR | ||||||
Components |
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Keywords | LIGASE/LIGASE INHIBITOR / Sina / beta sandwich / zinc finger / ubiquitin ligase / covalent inhibitor / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | Function and homology information R1/R6 cell fate commitment / sensory organ boundary specification / enteroendocrine cell differentiation / R7 cell fate commitment / sensory organ precursor cell fate determination / sevenless signaling pathway / Netrin-1 signaling / sensory organ development / beta-catenin destruction complex / ubiquitin conjugating enzyme binding ...R1/R6 cell fate commitment / sensory organ boundary specification / enteroendocrine cell differentiation / R7 cell fate commitment / sensory organ precursor cell fate determination / sevenless signaling pathway / Netrin-1 signaling / sensory organ development / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / negative regulation of Notch signaling pathway / ubiquitin-like ligase-substrate adaptor activity / canonical Wnt signaling pathway / anatomical structure morphogenesis / ubiquitin ligase complex / positive regulation of intrinsic apoptotic signaling pathway / Notch signaling pathway / visual perception / axon guidance / proteasomal protein catabolic process / protein catabolic process / negative regulation of canonical Wnt signaling pathway / RING-type E3 ubiquitin transferase / epidermal growth factor receptor signaling pathway / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / amyloid fibril formation / protein ubiquitination / cell cycle / positive regulation of apoptotic process / Amyloid fiber formation / apoptotic process / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Santelli, E. / Stebbins, J.L. / Feng, Y. / De, S.K. / Purves, A. / Motamedchaboki, K. / Wu, B. / Ronai, Z.A. / Liddington, R.C. / Pellecchia, M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2013 Title: Structure-based design of covalent siah inhibitors. Authors: Stebbins, J.L. / Santelli, E. / Feng, Y. / De, S.K. / Purves, A. / Motamedchaboki, K. / Wu, B. / Ronai, Z.A. / Liddington, R.C. / Pellecchia, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i7c.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i7c.ent.gz | 145.6 KB | Display | PDB format |
PDBx/mmJSON format | 4i7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/4i7c ftp://data.pdbj.org/pub/pdb/validation_reports/i7/4i7c | HTTPS FTP |
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-Related structure data
Related structure data | 4i7bC 4i7dSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21978.133 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 90-282) / Mutation: T156C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH1, HUMSIAH / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8IUQ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein/peptide | Type: Oligopeptide / Class: Inhibitor / Mass: 1709.155 Da / Num. of mol.: 2 / Fragment: Siah-binding peptide (UNP residues 113-125) / Mutation: T123W / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) References: UniProt: Q27934, modified protein phyllopod peptide BI-117C3 #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 3.9 Å3/Da / Density % sol: 68.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 65% MPD, 100 mM bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 24, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→60 Å / Num. all: 18292 / Num. obs: 18317 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.637 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4I7D Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 24.588 / SU ML: 0.222 / Isotropic thermal model: ISOTROPIC WITH TLS / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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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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