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Yorodumi- PDB-5l0y: Crystal Structure of a Sec72-ssa1 c-terminal peptide fusion protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l0y | ||||||
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Title | Crystal Structure of a Sec72-ssa1 c-terminal peptide fusion protein | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Protein translocation / TPR / C-terminal Ssa1 peptide / PEPTIDE BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chaetomium thermophilum (fungus) Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å | ||||||
Authors | Tripathi, A. / Rapoport, T.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Two alternative binding mechanisms connect the protein translocation Sec71-Sec72 complex with heat shock proteins. Authors: Tripathi, A. / Mandon, E.C. / Gilmore, R. / Rapoport, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l0y.cif.gz | 242 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l0y.ent.gz | 199.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l0y_validation.pdf.gz | 531.3 KB | Display | wwPDB validaton report |
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Full document | 5l0y_full_validation.pdf.gz | 568.4 KB | Display | |
Data in XML | 5l0y_validation.xml.gz | 44 KB | Display | |
Data in CIF | 5l0y_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/5l0y ftp://data.pdbj.org/pub/pdb/validation_reports/l0/5l0y | HTTPS FTP |
-Related structure data
Related structure data | 5l0wSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 18192.420 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus), (gene. exp.) Saccharomyces cerevisiae S288c (yeast) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0068610 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SH41 #2: Protein/peptide | Mass: 787.811 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: G0RYP6*PLUS |
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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: 2.46 Å3/Da / Density % sol: 49.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M ammonium citrate pH 7.0, 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→164.05 Å / Num. obs: 34691 / % possible obs: 99.3 % / Redundancy: 2 % / Net I/σ(I): 16 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L0W Resolution: 2.87→96.08 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.3 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.87→96.08 Å
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Refine LS restraints |
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LS refinement shell |
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