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Yorodumi- PDB-4y6k: Complex structure of presenilin homologue PSH bound to an inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y6k | ||||||
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Title | Complex structure of presenilin homologue PSH bound to an inhibitor | ||||||
Components | Uncharacterized protein PSH | ||||||
Keywords | MEMBRANE PROTEIN/INHIBITOR / Complex / Inhibitor / MEMBRANE PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information aspartic endopeptidase activity, intramembrane cleaving / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Methanoculleus marisnigri JR1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.855 Å | ||||||
Authors | Dang, S. / Wu, S. / Wang, J. / Shi, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Cleavage of amyloid precursor protein by an archaeal presenilin homologue PSH Authors: Dang, S. / Wu, S. / Wang, J. / Li, H. / Huang, M. / He, W. / Li, Y.M. / Wong, C.C. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y6k.cif.gz | 373.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y6k.ent.gz | 312.1 KB | Display | PDB format |
PDBx/mmJSON format | 4y6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y6k_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4y6k_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4y6k_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 4y6k_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/4y6k ftp://data.pdbj.org/pub/pdb/validation_reports/y6/4y6k | HTTPS FTP |
-Related structure data
Related structure data | 4hygS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 31879.260 Da / Num. of mol.: 4 / Mutation: D40N, E42S, A147E, V148P, A229V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanoculleus marisnigri JR1 (archaea) Strain: JR1 / Gene: Memar_1924 / Production host: Escherichia coli (E. coli) / References: UniProt: A3CWV0 #2: Chemical | |
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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: 3.92 Å3/Da / Density % sol: 68.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M Glycine pH 3.6, 0.2 M (NH4)2SO4, 20% (w/v) PEG500MME, 6% (w/v) Glycerol, 0.04% (w/v) Anapoe-C12E8,1% (w/v) N-heptyl-b-D-thioglucoside |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RIGAKU SATURN 724 / Detector: CCD / Date: Nov 29, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.85→50 Å / Num. obs: 7729 / % possible obs: 51 % / Redundancy: 6.5 % / Net I/σ(I): 8.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HYG Resolution: 3.855→48.203 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.69 / Phase error: 47.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.855→48.203 Å
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Refine LS restraints |
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LS refinement shell |
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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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