+Open data
-Basic information
Entry | Database: PDB / ID: 5grv | |||||||||
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Title | Crystal structure of homo-specific diabody | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / diabody / antibody fragment | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Kim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Lee, H. / Lee, J.O. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Sci Rep / Year: 2016 Title: Crystal structure of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface. Authors: Kim, J.H. / Song, D.H. / Youn, S.J. / Kim, J.W. / Cho, G. / Kim, S.C. / Lee, H. / Jin, M.S. / Lee, J.O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5grv.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5grv.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 5grv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/5grv ftp://data.pdbj.org/pub/pdb/validation_reports/gr/5grv | HTTPS FTP |
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-Related structure data
Related structure data | 5gruC 5grwC 5grxC 5gryC 5grzC 5gs0C 5gs1SC 5gs2C 5gs3C C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 13244.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) |
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#2: Antibody | Mass: 13640.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) |
#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: 3.98 Å3/Da / Density % sol: 69.07 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 2.3 M Sodium acetate, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 18614 / % possible obs: 99.9 % / Redundancy: 17.4 % / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.3→2.38 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GS1 Resolution: 2.3→36.232 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→36.232 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: 14.1079 Å / Origin y: -42.2497 Å / Origin z: -30.6164 Å
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Refinement TLS group | Selection details: all |