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Open data
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Basic information
Entry | Database: PDB / ID: 5kvw | |||||||||||||||
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Title | T. danielli thaumatin at 100K, Data set 1 | |||||||||||||||
![]() | Thaumatin-1 | |||||||||||||||
![]() | PLANT PROTEIN / Conformational variation / Radiation damage | |||||||||||||||
Function / homology | ![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational variation of proteins at room temperature is not dominated by radiation damage. Authors: Russi, S. / Gonzalez, A. / Kenner, L.R. / Keedy, D.A. / Fraser, J.S. / van den Bedem, H. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74 KB | Display | ![]() |
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PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.4 KB | Display | ![]() |
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Full document | ![]() | 464.3 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kulC ![]() 5kunC ![]() 5kuoC ![]() 5kuqC ![]() 5kurC ![]() 5kusC ![]() 5kuuC ![]() 5kuvC ![]() 5kuwC ![]() 5kuzC ![]() 5kv0C ![]() 5kv1C ![]() 5kv2C ![]() 5kv3C ![]() 5kv4C ![]() 5kv5C ![]() 5kv6C ![]() 5kv7C ![]() 5kvxC ![]() 5kvzC ![]() 5kw0C ![]() 5kw3C ![]() 5kw4C ![]() 5kw5C ![]() 5kw7C ![]() 5kw8C ![]() 5kxkC ![]() 5kxlC ![]() 5kxmC ![]() 5kxnC ![]() 5kxoC ![]() 5kxpC ![]() 5kxrC ![]() 5kxsC ![]() 5kxtC ![]() 5kxwC ![]() 5kxxC ![]() 5kxyC ![]() 5kxzC ![]() 5ky1C ![]() 1rqwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22227.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Chemical | ChemComp-TLA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (0.9 M SODIUM/POTASSIUM TARTRATE, 0.2 M AMMONIUM SULFATE, 15% GLYCEROL, 25% PEG 8000, 100 MM HEPES PH 7.3) AND PROTEIN (35 MG/ML) ...Details: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (0.9 M SODIUM/POTASSIUM TARTRATE, 0.2 M AMMONIUM SULFATE, 15% GLYCEROL, 25% PEG 8000, 100 MM HEPES PH 7.3) AND PROTEIN (35 MG/ML) IN THE SITTING DROP FORMAT. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 13, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.21549 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→31.613 Å / Num. all: 34655 / Num. obs: 34655 / % possible obs: 99 % / Redundancy: 4.1 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.05 / Rsym value: 0.044 / Net I/av σ(I): 10.091 / Net I/σ(I): 15.1 / Num. measured all: 141558 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RQW Resolution: 1.59→31.61 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.358 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.94 Å2 / Biso mean: 26.895 Å2 / Biso min: 14.56 Å2
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Refinement step | Cycle: final / Resolution: 1.59→31.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.631 Å / Total num. of bins used: 20
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