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Open data
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Basic information
Entry | Database: PDB / ID: 5aum | ||||||
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Title | Crystal structure of a Fab fragment with the ligand peptide | ||||||
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![]() | IMMUNE SYSTEM/PEPTIDE / Antibody / peptide ligand / protease / ELISA / Western blotting / IMMUNE SYSTEM-PEPTIDE complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kitago, Y. / Takagi, J. | ||||||
![]() | ![]() Title: Crystal structure of a Fab fragment with the ligand peptide Authors: Kitago, 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 | ![]() | 192.7 KB | Display | ![]() |
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PDB format | ![]() | 150.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bfoS S: Starting model for refinement |
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Similar structure data |
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Links
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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: 26009.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 25941.279 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein/peptide | Mass: 1328.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The modified TEV protease recognition sequence / Source: (synth.) ![]() #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 % PEG 2000 MME, 0.5 M NaCl, 0.1 M Tris-HCl pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jan 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 88376 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rsym value: 0.148 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 5.1 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BFO Resolution: 2.05→45.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.529 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.135 / 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: 26.895 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→45.69 Å
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