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Open data
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Basic information
Entry | Database: PDB / ID: 3l7f | |||||||||
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Title | Structure of IL-13 antibody H2L6, A humanized variant OF C836 | |||||||||
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![]() | IMMUNE SYSTEM / immunoglobulin fold / MONOCLONAL ANTIBODY | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. | |||||||||
![]() | ![]() Title: Human framework adaptation of a mouse anti-human IL-13 antibody. Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, ...Authors: Fransson, J. / Teplyakov, A. / Raghunathan, G. / Chi, E. / Cordier, W. / Dinh, T. / Feng, Y. / Giles-Komar, J. / Gilliland, G. / Lollo, B. / Malia, T.J. / Nishioka, W. / Obmolova, G. / Zhao, S. / Zhao, Y. / Swanson, R.V. / Almagro, J.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260 KB | Display | ![]() |
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PDB format | ![]() | 210.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.3 KB | Display | ![]() |
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Full document | ![]() | 504.6 KB | Display | |
Data in XML | ![]() | 48.1 KB | Display | |
Data in CIF | ![]() | 67.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l5wC ![]() 3l5xSC ![]() 4ps4C 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23487.115 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell (production host): Human embryonic kidney (HEK) 293 cells Production host: ![]() #2: Antibody | Mass: 24110.328 Da / Num. of mol.: 3 Fragment: FD fragment of the heavy chain, VH and CH1 domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell (production host): Human embryonic kidney (HEK) 293 cells Production host: ![]() #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES PH 6.5, 5% PEG 4K, 38% MPD; CRYO CONDITIONS: 0.1 M MES PH 6.5, 5% PEG 4K, 40% MPD, 15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 4, 2008 / Details: VARIMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→66.6 Å / Num. all: 56212 / Num. obs: 56212 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 92.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3L5X Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.473 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.483 / ESU R Free: 0.279 / Stereochemistry target values: Engh & Huber
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.279 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20
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