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- PDB-4g6k: Crystal structure of the therapeutic antibody binding fragment of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4g6k | ||||||
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Title | Crystal structure of the therapeutic antibody binding fragment of gevokizumab in its unbound state | ||||||
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![]() | IMMUNE SYSTEM / immunoglobulin fold / cytokine / interleukine-1beta | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blech, M. / Hoerer, S. | ||||||
![]() | ![]() Title: One target-two different binding modes: Structural insights into gevokizumab and canakinumab interactions to interleukin-1beta Authors: Blech, M. / Peter, D. / Fischer, P. / Bauer, M.M. / Hafner, M. / Zeeb, M. / Nar, 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 | ![]() | 186.5 KB | Display | ![]() |
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PDB format | ![]() | 147.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.8 KB | Display | ![]() |
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Full document | ![]() | 431.5 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g5zC ![]() 4g6jC ![]() 4g6mC ![]() 1pz5S ![]() 3bkjS 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: 23420.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) homo Sapiens, Mus musculus / Cell line (production host): CHO / Production host: ![]() ![]() |
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#2: Antibody | Mass: 23371.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) homo Sapiens, Mus musculus / Cell line (production host): CHO / Production host: ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 14.3% w/v PEG 3350 and 0.14M tri-sodium citrate at pH 5.0 equilibrated against 24% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→57.4 Å / Num. all: 284279 / Num. obs: 41364 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 24.43 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.084 / Net I/σ(I): 19.4 |
Reflection shell | Highest resolution: 1.9 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PZ5 and 3BKJ Resolution: 1.9→27.75 Å / Cor.coef. Fo:Fc: 0.9458 / Cor.coef. Fo:Fc free: 0.9335 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 28.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.212 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→27.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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