+Open data
-Basic information
Entry | Database: PDB / ID: 6xud | ||||||
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Title | Apo Ab 1116NS19.9 | ||||||
Components |
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Keywords | ANTITUMOR PROTEIN / Pancreatic cancer / CA19-9 binder / Diagnosis / Immunotherapy reagent | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Diskin, R. / Borenstein-Katz, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Biomolecular Recognition of the Glycan Neoantigen CA19-9 by Distinct Antibodies. Authors: Borenstein-Katz, A. / Warszawski, S. / Amon, R. / Eilon, M. / Cohen-Dvashi, H. / Leviatan Ben-Arye, S. / Tasnima, N. / Yu, H. / Chen, X. / Padler-Karavani, V. / Fleishman, S.J. / Diskin, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xud.cif.gz | 264.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xud.ent.gz | 217.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xud_validation.pdf.gz | 246.5 KB | Display | wwPDB validaton report |
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Full document | 6xud_full_validation.pdf.gz | 247.6 KB | Display | |
Data in XML | 6xud_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 6xud_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/6xud ftp://data.pdbj.org/pub/pdb/validation_reports/xu/6xud | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 23799.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23759.486 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / 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: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: n-Octyl-b-D-glucoside, Na citrate tri di pH 5.5, PEG 3,350, ethylen glycol 7.5% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.51→45.903 Å / Num. obs: 155178 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.044 / Rrim(I) all: 0.134 / Net I/σ(I): 9.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: holo Ab 1116NS19.9 Resolution: 1.51→45.903 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.99
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.79 Å2 / Biso mean: 25.101 Å2 / Biso min: 9.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.51→45.903 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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