+Open data
-Basic information
Entry | Database: PDB / ID: 5i0z | ||||||
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Title | Crystal structure of the single domain catalytic antibody 3D8-VH | ||||||
Components | catalytic DNA antibody | ||||||
Keywords | IMMUNE SYSTEM / 3D8 scFv / 3D8-VH | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Park, S.Y. / Kim, J.S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the single domain catalytic antibody 3D8-VH Authors: Park, S.Y. / Kim, B.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i0z.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i0z.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 5i0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/5i0z ftp://data.pdbj.org/pub/pdb/validation_reports/i0/5i0z | HTTPS FTP |
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-Related structure data
Related structure data | 2gkiS S: Starting model for refinement |
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Similar structure data |
-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: 15814.971 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #2: 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: 1.97 Å3/Da / Density % sol: 37.42 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 30 % (w/v) PEG 8000 and 0.1 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.24 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 16712 / % possible obs: 96.3 % / Redundancy: 2.7 % / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.9→2 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GKI Resolution: 1.9→37.402 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.27 Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→37.402 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -16.2106 Å / Origin y: 3.1102 Å / Origin z: -0.0331 Å
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Refinement TLS group | Selection details: all |