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Yorodumi- PDB-3d9h: Crystal Structure of the Splice Variant of Human ASB9 (hASB9-2), ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d9h | ||||||
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Title | Crystal Structure of the Splice Variant of Human ASB9 (hASB9-2), an Ankyrin Repeat Protein | ||||||
Components | cDNA FLJ77766, highly similar to Homo sapiens ankyrin repeat and SOCS box-containing 9 (ASB9), transcript variant 2, mRNA | ||||||
Keywords | STRUCTURAL PROTEIN / PROTEIN BINDING / ASB9 / ANK repeat / L-shaped / alpha-helices | ||||||
Function / homology | Function and homology information post-translational protein modification / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / protein ubiquitination / intracellular signal transduction / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Fei, X. / Gu, X. / Fan, S. / Zhang, C. / Ji, C. | ||||||
Citation | Journal: To be published Title: Crystal Structure of the Splice Variant of Human ASB9 (hASB9-2), an Ankyrin Repeat Protein Authors: Fei, X. / Gu, X. / Fan, S. / Zhang, Y. / Li, F. / Zhang, C. / Gong, W. / Mao, Y. / Ji, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d9h.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d9h.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 3d9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/3d9h ftp://data.pdbj.org/pub/pdb/validation_reports/d9/3d9h | HTTPS FTP |
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-Related structure data
Related structure data | 1n11S 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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Details | THERE ARE SOME CLOSE CONTACTS BASED ON CRYSTAL SYMMETRY IN THIS ENTRY. THEREFORE, PISA CAN NOT SUGGEST ANY POSSIBLE QUATERNARY STRUCTURE. PLEASE SEE THE DETAILS IN REMARK 3. |
-Components
#1: Protein | Mass: 30425.484 Da / Num. of mol.: 1 / Mutation: A207V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: hASB9-2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: A8K8A5, UniProt: Q96DX5*PLUS |
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#2: 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: 2.96 Å3/Da / Density % sol: 58.41 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Imidazole pH 6.5, 1.0M Sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 19383 / Num. obs: 19367 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 44.3 / Num. measured all: 709934 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 6.5 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N11 Resolution: 2.2→35.85 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.253 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The segments from Phe19 to Ser26 in two crystallographic symmetry-related molecules are related by a crystallographic 2-fold axis, and ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The segments from Phe19 to Ser26 in two crystallographic symmetry-related molecules are related by a crystallographic 2-fold axis, and their densities overlap. So the depositors had to ignore the close contacts between these two segments given by validation software and assigned the occupancy of each segment to 0.5 to avoid clash.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.468 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→35.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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