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- PDB-5v46: Crystal structure of the I113M, F270M, K291M, L308M mutant of SR1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5v46 | ||||||
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Title | Crystal structure of the I113M, F270M, K291M, L308M mutant of SR1 domain of human sacsin | ||||||
![]() | Sacsin | ||||||
![]() | CHAPERONE / alpha-beta sandwich / Bergerat fold | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Menade, M. / Kozlov, G. / Gehring, K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210 KB | Display | ![]() |
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PDB format | ![]() | 170.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.2 KB | Display | ![]() |
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Full document | ![]() | 441.9 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v44C ![]() 5v45SC ![]() 5v47C ![]() 5vsxC ![]() 5vszC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 28846.482 Da / Num. of mol.: 2 / Fragment: UNP residues 89-336 / Mutation: I113M,F270M,K291M,L308M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.32 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 5, 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: 1.8→50 Å / Num. obs: 43323 / % possible obs: 99.9 % / Redundancy: 15.2 % / Rsym value: 0.096 / Net I/σ(I): 47 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 15 % / Mean I/σ(I) obs: 6.4 / Rsym value: 0.592 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5V45 Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.532 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131
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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: 21.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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