[English] 日本語
Yorodumi- PDB-6dez: Anti-phosphotyrosine antibody PY20-4D5 Fab complexed with sulfate -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dez | ||||||
---|---|---|---|---|---|---|---|
Title | Anti-phosphotyrosine antibody PY20-4D5 Fab complexed with sulfate | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Antibody / RECOMBINATION | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Model details | Antibody | ||||||
Authors | Mou, K. / Leung, K. / Wells, J.A. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Engineering Improved Antiphosphotyrosine Antibodies Based on an Immunoconvergent Binding Motif. Authors: Mou, Y. / Zhou, X.X. / Leung, K. / Martinko, A.J. / Yu, J.Y. / Chen, W. / Wells, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6dez.cif.gz | 169.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dez.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 6dez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dez_validation.pdf.gz | 468 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6dez_full_validation.pdf.gz | 483.6 KB | Display | |
Data in XML | 6dez_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 6dez_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/6dez ftp://data.pdbj.org/pub/pdb/validation_reports/de/6dez | HTTPS FTP |
-Related structure data
Related structure data | 6df0C 6df1C 6df2C 1bj1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Antibody | Mass: 26951.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): C43 #2: Antibody | Mass: 28786.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): C43 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.02 % / Mosaicity: 1.1 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG4000 and 0.336M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 2016 |
Radiation | Monochromator: Water-cooled flat double Si(111) Khozu monochromator (DCM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→74.3 Å / Num. obs: 20773 / % possible obs: 99.9 % / Redundancy: 17.9 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.143 / Rrim(I) all: 0.373 / Net I/σ(I): 4.8 / Num. measured all: 397240 / Scaling rejects: 202 |
Reflection shell | Resolution: 3.2→3.36 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.454 / Num. unique obs: 4345 / CC1/2: 0.105 / Rpim(I) all: 2.758 / Rrim(I) all: 6.731 / % possible all: 99.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1bj1 Resolution: 3.2→19.999 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.99 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→19.999 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|