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Open data
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Basic information
Entry | Database: PDB / ID: 5xcx | ||||||
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Title | Crystal structure of TS2/16 Fv-clasp fragment | ||||||
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![]() | IMMUNE SYSTEM / antibody fragment / Fv-clasp | ||||||
Function / homology | p53, subunit A / p53-like tetramerisation domain / Few Secondary Structures / Irregular / PHOSPHATE ION![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arimori, T. / Takagi, J. | ||||||
![]() | ![]() Title: Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability Authors: Arimori, T. / Kitago, Y. / Umitsu, M. / Fujii, Y. / Asaki, R. / Tamura-Kawakami, K. / Takagi, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.4 KB | Display | ![]() |
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PDB format | ![]() | 119.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.5 KB | Display | ![]() |
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Full document | ![]() | 458.8 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xcqC ![]() 5xcrC ![]() 5xcsC ![]() 5xctC ![]() 5xcuC ![]() 5xcvC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 19463.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() |
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#2: Antibody | Mass: 18270.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ? Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() |
-Non-polymers , 4 types, 177 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 1.2M NaH2PO4/0.8M K2HPO4, 0.1M CAPS (pH10.5), 0.2M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→47.05 Å / Num. obs: 27142 / % possible obs: 99.6 % / Redundancy: 15.8 % / Rsym value: 0.129 / Net I/σ(I): 18.42 |
Reflection shell | Resolution: 2.04→2.17 Å / Redundancy: 15.9 % / Mean I/σ(I) obs: 3.94 / Rsym value: 0.967 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.934 Å2
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Refinement step | Cycle: 1 / Resolution: 2.04→47.05 Å
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Refine LS restraints |
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