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Yorodumi- PDB-5v45: Crystal structure of the F270M, K291M, L318M mutant of SR1 domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v45 | ||||||
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Title | Crystal structure of the F270M, K291M, L318M mutant of SR1 domain of human sacsin | ||||||
Components | Sacsin | ||||||
Keywords | CHAPERONE / alpha-beta sandwich / Bergerat fold | ||||||
Function / homology | Function and homology information negative regulation of inclusion body assembly / cell body fiber / proteasome binding / Hsp70 protein binding / protein folding / protein-folding chaperone binding / axon / dendrite / mitochondrion / identical protein binding ...negative regulation of inclusion body assembly / cell body fiber / proteasome binding / Hsp70 protein binding / protein folding / protein-folding chaperone binding / axon / dendrite / mitochondrion / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Menade, M. / Kozlov, G. / Gehring, K. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structures of ubiquitin-like (Ubl) and Hsp90-like domains of sacsin provide insight into pathological mutations. Authors: Menade, M. / Kozlov, G. / Trempe, J.F. / Pande, H. / Shenker, S. / Wickremasinghe, S. / Li, X. / Hojjat, H. / Dicaire, M.J. / Brais, B. / McPherson, P.S. / Wong, M.J.H. / Young, J.C. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v45.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v45.ent.gz | 166.1 KB | Display | PDB format |
PDBx/mmJSON format | 5v45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/5v45 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/5v45 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28781.553 Da / Num. of mol.: 2 / Fragment: UNP residues 89-336 / Mutation: F270M, K291M, L318M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SACS, KIAA0730 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NZJ4 #2: 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: 2.16 Å3/Da / Density % sol: 43.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 28% PEG 3350, 0.2 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 32566 / % possible obs: 96.19 % / Redundancy: 7.9 % / Rsym value: 0.091 / Net I/σ(I): 43.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2240 / Rsym value: 0.456 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.312 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.152
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.272 Å2
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Refinement step | Cycle: 1 / Resolution: 1.91→50 Å
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Refine LS restraints |
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