+Open data
-Basic information
Entry | Database: PDB / ID: 6t2j | ||||||
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Title | dAb3 | ||||||
Components | Single domain antibodySingle-domain antibody | ||||||
Keywords | IMMUNE SYSTEM / Human Single Domain Antibody | ||||||
Function / homology | PHOSPHATE ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Tsai, Y.-C.I. / House, D. / Rittinger, K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cell Chem Biol / Year: 2020 Title: Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases. Authors: Tsai, Y.I. / Johansson, H. / Dixon, D. / Martin, S. / Chung, C.W. / Clarkson, J. / House, D. / Rittinger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t2j.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t2j.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 6t2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/6t2j ftp://data.pdbj.org/pub/pdb/validation_reports/t2/6t2j | HTTPS FTP |
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-Related structure data
Related structure data | 6sc5C 6sc6C 6sc7C 6sc8C 6sc9C 1ohqS 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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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 13073.577 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-PO4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.31 Å3/Da / Density % sol: 46.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium dihydrogen phosphate, Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→43.42 Å / Num. obs: 26230 / % possible obs: 99.78 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.07439 / Net I/σ(I): 11.36 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.3836 / Num. unique obs: 2586 / % possible all: 99.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OHQ Resolution: 1.7→43.42 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5082
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→43.42 Å
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Refine LS restraints |
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LS refinement shell |
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