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Open data
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Basic information
Entry | Database: PDB / ID: 5gis | |||||||||
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Title | Crystal structure of a Fab fragment with its ligand peptide | |||||||||
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Function / homology | ![]() Citric acid cycle (TCA cycle) / isocitrate metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kitago, Y. / Kaneko, K.K. / Ogasawara, S. / Kato, Y. / Takagi, J. | |||||||||
![]() | ![]() Title: Structural basis for multi-specific peptide recognition by the anti-IDH1/2 monoclonal antibody, MsMab-1. Authors: Kitago, Y. / Kaneko, M.K. / Ogasawara, S. / Kato, Y. / Takagi, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.1 KB | Display | ![]() |
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PDB format | ![]() | 76.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5girSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 25712.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Antibody | Mass: 26006.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Protein/peptide | Mass: 1756.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.08 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Imidazole-HCl pH 6.5, 2.1 M Ammonium Sulfate, 0.2 M Potassium/Sodium Tartrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.93→45 Å / Num. obs: 34050 / % possible obs: 98.2 % / Redundancy: 5.8 % / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.93→2.04 Å |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5GIR Resolution: 1.93→44.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.71 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.578 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→44.99 Å
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Refine LS restraints |
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