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Yorodumi- PDB-6dzf: Orthorhombic trypsin cryocooled to 100 K with 20% xylose as cryop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dzf | ||||||
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Title | Orthorhombic trypsin cryocooled to 100 K with 20% xylose as cryoprotectant | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Juers, D.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order. Authors: Juers, D.H. / Farley, C.A. / Saxby, C.P. / Cotter, R.A. / Cahn, J.K.B. / Holton-Burke, R.C. / Harrison, K. / Wu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dzf.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dzf.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 6dzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/6dzf ftp://data.pdbj.org/pub/pdb/validation_reports/dz/6dzf | HTTPS FTP |
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-Related structure data
Related structure data | 5un3C 5uu7C 5uu8C 5uu9C 5uuaC 5uubC 5uucC 5uudC 5uueC 6avlC 6b6nC 6b6oC 6b6pC 6b6qSC 6b6rC 6b6sC 6b6tC 6d5nC 6d5oC 6d5pC 6d5qC 6d5rC 6d5sC 6d5tC 6d5uC 6d6eC 6d6fC 6d6gC 6d6hC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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#5: Sugar | ChemComp-XYS / |
-Non-polymers , 4 types, 85 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-BEN / |
#4: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: Well: 25% PEG 8K, 0.2 M AmSO4, 0.1 M benzamidine HCl, 0.1 M Tris buffer pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Mar 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→13.5 Å / Num. obs: 10574 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.41 Å2 / CC1/2: 0.61 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 2.2→2.32 Å / Mean I/σ(I) obs: 1.1 / CC1/2: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6B6Q Resolution: 2.2→13.45 Å / SU ML: 0.9013 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 50.9541 / Stereochemistry target values: GeoStd + Monomer Library
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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: 28.74 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→13.45 Å
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Refine LS restraints |
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LS refinement shell |
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