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Yorodumi- PDB-6wgk: Fab portion of dupilumab with Crystal Kappa design and intrachain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wgk | ||||||
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Title | Fab portion of dupilumab with Crystal Kappa design and intrachain disulfide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Dupilumab / hIL4R | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Druzina, Z. / Atwell, S. / Pustilnik, A. / Antonysamy, S. / Ho, C. / Lieu, R. / Hendle, J. / Benach, J. / Wang, J. | ||||||
Citation | Journal: Plos One / Year: 2020 Title: Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing. Authors: Lieu, R. / Antonysamy, S. / Druzina, Z. / Ho, C. / Kang, N.R. / Pustilnik, A. / Wang, J. / Atwell, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wgk.cif.gz | 344.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wgk.ent.gz | 277.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/6wgk ftp://data.pdbj.org/pub/pdb/validation_reports/wg/6wgk | HTTPS FTP |
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-Related structure data
Related structure data | 6wg8C 6wgbSC 6wgjC 6wglC 6wioC 6wirC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25230.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 23803.469 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.07 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100mM Tris HCl pH 8.5, 20% PEG MME 2K , 200mM Trimethylamine N-oxide dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Feb 5, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→109.5 Å / Num. obs: 225219 / % possible obs: 95.5 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 12.6 / Num. measured all: 809633 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WGB Resolution: 1.62→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.087 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.1 / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 83.12 Å2 / Biso mean: 28.25 Å2 / Biso min: 13.26 Å2
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Refinement step | Cycle: final / Resolution: 1.62→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.621→1.663 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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