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- PDB-3nfp: Crystal structure of the Fab fragment of therapeutic antibody dac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nfp | ||||||
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Title | Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain | ||||||
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Function / homology | ![]() regulation of T cell tolerance induction / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, H. / Wang, J. / Du, J. / Zhong, C. / Guo, Y. / Ding, J. | ||||||
![]() | ![]() Title: Structural basis of immunosuppression by the therapeutic antibody daclizumab Authors: Yang, H. / Wang, J. / Du, J. / Zhong, C. / Zhang, D. / Guo, H. / Guo, Y. / Ding, 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 | ![]() | 393.9 KB | Display | ![]() |
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PDB format | ![]() | 319.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3nfsSC S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23034.682 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: purchased from Roche, expressed in a mammalian expression system #2: Antibody | Mass: 23134.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: purchased from Roche, expressed in a mammalian expression system #3: Protein | ![]() Mass: 25388.348 Da / Num. of mol.: 2 / Fragment: UNP residues 22-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.57 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→50 Å / Num. obs: 31671 / % possible obs: 95.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3NFS Resolution: 2.86→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.67 Å2 / Biso mean: 69.528 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.86→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.863→2.937 Å / Total num. of bins used: 20
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