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Yorodumi- PDB-4hyd: Structure of a presenilin family intramembrane aspartate protease... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hyd | ||||||
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Title | Structure of a presenilin family intramembrane aspartate protease in C2221 space group | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Methanoculleus marisnigri JR1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.8 Å | ||||||
Authors | Li, X. / Dang, S. / Yan, C. / Wang, J. / Shi, Y. | ||||||
Citation | Journal: Nature / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hyd.cif.gz | 375.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hyd.ent.gz | 316.7 KB | Display | PDB format |
PDBx/mmJSON format | 4hyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hyd_validation.pdf.gz | 468.5 KB | Display | wwPDB validaton report |
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Full document | 4hyd_full_validation.pdf.gz | 520.8 KB | Display | |
Data in XML | 4hyd_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 4hyd_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/4hyd ftp://data.pdbj.org/pub/pdb/validation_reports/hy/4hyd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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: ATCC 35101 / DSM 1498 / JR1 / Gene: Memar_1924 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3CWV0 |
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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: 3.45 Å3/Da / Density % sol: 64.34 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.07171, 1.05384, 1.07206 | ||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2011 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.8→50 Å / Num. obs: 15330 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 3.8→31.577 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 53.18 / Stereochemistry target values: MLHL
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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: 3.8→31.577 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0 / Total num. of bins used: 5
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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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