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Open data
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Basic information
Entry | Database: PDB / ID: 5grw | |||||||||
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Title | Crystal structure of homo-specific diabody | |||||||||
![]() | homo-specific diabody protein | |||||||||
![]() | IMMUNE SYSTEM / diabody / antibody fragment | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Lee, H. / Lee, J.O. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface. Authors: Kim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Kim, S.C. / Lee, H. / Jin, M.S. / Lee, J.O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182 KB | Display | ![]() |
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PDB format | ![]() | 144.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 451.8 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 25.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gruC ![]() 5grvC ![]() 5grxC ![]() 5gryC ![]() 5grzC ![]() 5gs0C ![]() 5gs1SC ![]() 5gs2C ![]() 5gs3C 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: Antibody | Mass: 26900.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.29 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M Sodium citrate pH 4.5, 0.3 M Ammonium acetate, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 16796 / % possible obs: 98.6 % / Redundancy: 3.5 % / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.8→2.9 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GS1 Resolution: 2.8→37.62 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→37.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -28.4493 Å / Origin y: 62.4884 Å / Origin z: 19.6426 Å
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Refinement TLS group | Selection details: all |