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- PDB-4hyg: Structure of a presenilin family intramembrane aspartate protease... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hyg | ||||||
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Title | Structure of a presenilin family intramembrane aspartate protease in C222 space group | ||||||
![]() | Putative uncharacterized protein | ||||||
![]() | MEMBRANE PROTEIN / protease | ||||||
Function / homology | Signal-peptide peptidase, presenilin aspartyl protease / Signal-peptide peptidase, presenilin aspartyl protease / Presenilin/signal peptide peptidase / Presenilin, signal peptide peptidase, family / aspartic endopeptidase activity, intramembrane cleaving / identical protein binding / membrane / Signal peptide peptidase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, X. / Dang, S. / Yan, C. / Wang, J. / Shi, Y. | ||||||
![]() | ![]() Title: Structure of a presenilin family intramembrane aspartate protease Authors: Li, X. / Dang, S. / Yan, C. / Gong, X. / Wang, J. / Shi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 371.2 KB | Display | ![]() |
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PDB format | ![]() | 313.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.5 KB | Display | ![]() |
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Full document | ![]() | 520.3 KB | Display | |
Data in XML | ![]() | 38.5 KB | Display | |
Data in CIF | ![]() | 52 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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.) ![]() Strain: ATCC 35101 / DSM 1498 / JR1 / Gene: Memar_1924 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: 0.1M Glycine, 0.2M (NH4)2SO4, 20%(w/v) PEG500MME, 6%(w/v) Glycerol, 0.04%(w/v) Anapoe-C12E8, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 24, 2012 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.3→50 Å / Num. obs: 24686 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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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: 3.32→49.108 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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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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