+Open data
-Basic information
Entry | Database: PDB / ID: 7jkb | ||||||
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Title | 2xVH Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / 2xVH / Fab | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Lord, D.M. / Zhou, Y.F. | ||||||
Citation | Journal: Antibodies / Year: 2020 Title: Bringing the Heavy Chain to Light: Creating a Symmetric, Bivalent IgG-Like Bispecific. Authors: Ramasubramanian, A. / Tennyson, R. / Magnay, M. / Kathuria, S. / Travaline, T. / Jain, A. / Lord, D.M. / Salemi, M. / Sullivan, C. / Magnay, T. / Hu, J. / Bric-Furlong, E. / Rival, P. / ...Authors: Ramasubramanian, A. / Tennyson, R. / Magnay, M. / Kathuria, S. / Travaline, T. / Jain, A. / Lord, D.M. / Salemi, M. / Sullivan, C. / Magnay, T. / Hu, J. / Bric-Furlong, E. / Rival, P. / Zhou, Y. / Hoffmann, D. / Brondyk, W. / Radosevic, K. / Chowdhury, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jkb.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jkb.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 7jkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jkb_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 7jkb_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 7jkb_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 7jkb_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/7jkb ftp://data.pdbj.org/pub/pdb/validation_reports/jk/7jkb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 24145.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 25552.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.11 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1M lithium chloride, 0.1M citric acid pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2018 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.55→48.75 Å / Num. obs: 20965 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.8 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: modeled Fab Resolution: 2.55→48.75 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.69 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 160.94 Å2 / Biso mean: 81.4778 Å2 / Biso min: 38.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→48.75 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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