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Yorodumi- PDB-8hyg: Crystal structure of protease-associated domain of Arabidopsis va... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hyg | ||||||||||||||||||
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Title | Crystal structure of protease-associated domain of Arabidopsis vacuolar sorting receptor 1 at pH 4.6 | ||||||||||||||||||
Components | Vacuolar-sorting receptor 1 | ||||||||||||||||||
Keywords | PROTEIN TRANSPORT / VSR / Vacuolar Sorting / Protease-associated domain | ||||||||||||||||||
Function / homology | Function and homology information amino-terminal vacuolar sorting propeptide binding / Golgi to vacuole transport / clathrin-coated vesicle membrane / vacuolar transport / protein targeting to vacuole / trans-Golgi network / late endosome / Golgi membrane / calcium ion binding / Golgi apparatus ...amino-terminal vacuolar sorting propeptide binding / Golgi to vacuole transport / clathrin-coated vesicle membrane / vacuolar transport / protein targeting to vacuole / trans-Golgi network / late endosome / Golgi membrane / calcium ion binding / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||||||||
Authors | Tsao, H.E. / Lui, S.N. / Wong, K.B. | ||||||||||||||||||
Funding support | Hong Kong, 5items
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Citation | Journal: To Be Published Title: Crystal structure of protease-associated domain of Arabidopsis vacuolar sorting receptor 1 at pH 4.6 Authors: Tsao, H.E. / Lui, S.N. / Wong, K.B. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hyg.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hyg.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 8hyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hyg_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 8hyg_full_validation.pdf.gz | 463 KB | Display | |
Data in XML | 8hyg_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 8hyg_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/8hyg ftp://data.pdbj.org/pub/pdb/validation_reports/hy/8hyg | HTTPS FTP |
-Related structure data
Related structure data | 4tjvS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17831.242 Da / Num. of mol.: 1 / Fragment: Protease associated domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VSR1, BP80B, ELP, ELP1, At3g52850, F8J2.20 / Production host: Escherichia coli (E. coli) / References: UniProt: P93026 |
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-Non-polymers , 5 types, 81 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.09 Å3/Da / Density % sol: 41.09 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Sep 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→37.42 Å / Num. obs: 19332 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.2 % / Num. unique obs: 954 / CC1/2: 0.933 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TJV Resolution: 1.6→31.8 Å / SU ML: 0.1838 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.4394 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→31.8 Å
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Refine LS restraints |
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LS refinement shell |
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