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Yorodumi- PDB-6b6p: Orthorhombic trypsin cryocooled to 100 K with 30% xylose as cryop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b6p | |||||||||
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Title | Orthorhombic trypsin cryocooled to 100 K with 30% xylose as cryoprotectant | |||||||||
Components | Cationic trypsin | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.00005891372 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 | 6b6p.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b6p.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 6b6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b6p_validation.pdf.gz | 460.2 KB | Display | wwPDB validaton report |
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Full document | 6b6p_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 6b6p_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 6b6p_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/6b6p ftp://data.pdbj.org/pub/pdb/validation_reports/b6/6b6p | HTTPS FTP |
-Related structure data
Related structure data | 5un3C 5uu7C 5uu8C 5uu9C 5uuaC 5uubC 5uucC 5uudC 5uueC 6avlC 6b6nC 6b6oC 6b6qC 6b6rC 6b6sC 6b6tC 6d5nC 6d5oC 6d5pC 6d5qC 6d5rC 6d5sC 6d5tC 6d5uC 6d6eC 6d6fC 6d6gC 6d6hC 6dzfC 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 , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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-Sugars , 2 types, 2 molecules
#5: Sugar | ChemComp-XYP / |
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#6: Sugar | ChemComp-XYS / |
-Non-polymers , 4 types, 253 molecules
#2: Chemical | ChemComp-CA / | ||
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#3: Chemical | ChemComp-BEN / | ||
#4: Chemical | #7: 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: 2.27 Å3/Da / Density % sol: 45.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Well: 25% PEG 8K, 0.2 M AmSO4, 0.1 M benzamidine Hal, 0.1 M Tris buffer pH 8.0 Protein: 40 mg/mL in water |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Apr 13, 2016 |
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→13.8 Å / Num. obs: 14610 / % possible obs: 98.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 8.60145398473 Å2 / CC1/2: 1 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 2→2.11 Å / Mean I/σ(I) obs: 16.1 / Num. unique obs: 2092 / CC1/2: 1 |
-Processing
Software |
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Refinement | Resolution: 2.00005891372→13.3812821704 Å / SU ML: 0.148133556728 / Cross valid method: FREE R-VALUE / σ(F): 1.36738589633 / Phase error: 14.6345448023
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.6571035826 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00005891372→13.3812821704 Å
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Refine LS restraints |
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LS refinement shell |
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