[English] 日本語
Yorodumi- PDB-3gje: Rational development of high-affinity T-cell receptor-like antibodies -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gje | ||||||
---|---|---|---|---|---|---|---|
Title | Rational development of high-affinity T-cell receptor-like antibodies | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Antibody / pMHC / immune recognition | ||||||
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 | Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. ...Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. / Knuth, A. / Abken, H. / Hombach, A.A. / Cerundolo, V. / Jones, E.Y. / Renner, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Rational development of high-affinity T-cell receptor-like antibodies Authors: Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. / Knuth, A. / Abken, H. / Hombach, A.A. / ...Authors: Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. / Knuth, A. / Abken, H. / Hombach, A.A. / Cerundolo, V. / Jones, E.Y. / Renner, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gje.cif.gz | 178.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gje.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gje_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3gje_full_validation.pdf.gz | 478.2 KB | Display | |
Data in XML | 3gje_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 3gje_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/3gje ftp://data.pdbj.org/pub/pdb/validation_reports/gj/3gje | HTTPS FTP |
-Related structure data
Related structure data | 3gjfC 3haeC 1rzfS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 22723.002 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHEN / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 #2: Antibody | Mass: 23066.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHEN / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.27 % |
---|---|
Crystal grow | Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 44489 / Num. obs: 44489 / Observed criterion σ(F): 428360 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RZF Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.471 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.399 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.303→2.362 Å / Total num. of bins used: 20
|