+Open data
-Basic information
Entry | Database: PDB / ID: 5aum | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a Fab fragment with the ligand peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM/PEPTIDE / Antibody / peptide ligand / protease / ELISA / Western blotting / IMMUNE SYSTEM-PEPTIDE complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Rattus (rat) Potyviridae (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Kitago, Y. / Takagi, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of a Fab fragment with the ligand peptide Authors: Kitago, Y. / Takagi, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5aum.cif.gz | 192.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5aum.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 5aum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aum_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5aum_full_validation.pdf.gz | 454.2 KB | Display | |
Data in XML | 5aum_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 5aum_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/5aum ftp://data.pdbj.org/pub/pdb/validation_reports/au/5aum | HTTPS FTP |
-Related structure data
Related structure data | 1bfoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Antibody | Mass: 26009.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus (rat) / Cell: hybridoma / Cell (production host): hybridoma / Production host: Mammalia (mammals) #2: Antibody | Mass: 25941.279 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus (rat) / Cell: hybridoma / Cell (production host): hybridoma / Production host: Mammalia (mammals) #3: Protein/peptide | Mass: 1328.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The modified TEV protease recognition sequence / Source: (synth.) Potyviridae (virus) #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.34 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→45.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|