+Open data
-Basic information
Entry | Database: PDB / ID: 4qt6 | ||||||
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Title | Crystal structure of the SPRY domain of human HERC1 | ||||||
Components | Probable E3 ubiquitin-protein ligase HERC1 | ||||||
Keywords | TRANSPORT PROTEIN / SPRY / B30.2 / HERC1 / E3 ubiquitin ligase / structural genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information cerebellar Purkinje cell differentiation / corpus callosum development / HECT-type E3 ubiquitin transferase / neuromuscular process controlling balance / negative regulation of autophagy / guanyl-nucleotide exchange factor activity / autophagy / ubiquitin-protein transferase activity / neuron projection development / Antigen processing: Ubiquitination & Proteasome degradation ...cerebellar Purkinje cell differentiation / corpus callosum development / HECT-type E3 ubiquitin transferase / neuromuscular process controlling balance / negative regulation of autophagy / guanyl-nucleotide exchange factor activity / autophagy / ubiquitin-protein transferase activity / neuron projection development / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / Golgi apparatus / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.64 Å | ||||||
Authors | Dong, A. / Hu, J. / Guan, X. / Wernimont, A. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the SPRY domain of human HERC1 Authors: Hu, J. / Dong, A. / Guan, X. / Wernimont, A. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qt6.cif.gz | 48 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qt6.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 4qt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/4qt6 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/4qt6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 17992.352 Da / Num. of mol.: 1 / Fragment: SPRY domain (UNP residues 2035-2192) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HERC1 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R / References: UniProt: Q15751 | ||||
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#2: Chemical | ChemComp-ARF / #3: Chemical | ChemComp-UNX / #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: 2.3 Å3/Da / Density % sol: 46.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.5 uL protein (mixed 1:700 w/w chymotrypsin:protein before setup) + 0.5 uL well solution (16% w/v PEG 8000, 0.04 M potassium phosphate monobasic, 20% v/v glycerol) + 0.1 uL 40% formamide ...Details: 0.5 uL protein (mixed 1:700 w/w chymotrypsin:protein before setup) + 0.5 uL well solution (16% w/v PEG 8000, 0.04 M potassium phosphate monobasic, 20% v/v glycerol) + 0.1 uL 40% formamide (4% final concentration), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5406 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 26, 2014 / Details: VeriMax HF | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SAD / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 16.1 % / Number: 327384 / Rmerge(I) obs: 0.047 / Χ2: 1.05 / D res high: 1.64 Å / D res low: 50 Å / Num. obs: 20328 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.64→50 Å / Num. obs: 20404 / % possible obs: 99.9 % / Redundancy: 27.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.08 / Net I/σ(I): 80.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.64→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.693 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.097 / 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 max: 59.93 Å2 / Biso mean: 24.467 Å2 / Biso min: 14.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.682 Å / Total num. of bins used: 20
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