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Yorodumi- PDB-6df0: anti-phosphotyrosine antibody 4G10-4D5 Fab complexed with sulfate -
+Open data
-Basic information
Entry | Database: PDB / ID: 6df0 | ||||||
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Title | anti-phosphotyrosine antibody 4G10-4D5 Fab complexed with sulfate | ||||||
Components |
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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: 2.3 Å | ||||||
Model details | Antibody | ||||||
Authors | Mou, K. / Leung, K. / Wells, J.A. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6df0.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6df0.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 6df0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6df0_validation.pdf.gz | 804.9 KB | Display | wwPDB validaton report |
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Full document | 6df0_full_validation.pdf.gz | 806.3 KB | Display | |
Data in XML | 6df0_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 6df0_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/6df0 ftp://data.pdbj.org/pub/pdb/validation_reports/df/6df0 | HTTPS FTP |
-Related structure data
Related structure data | 6dezC 6df1C 6df2C 1bj1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 26829.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 27883.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG4000, 0.2M ammonium sulfate, and 0.1M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: 1.82→85.65 Å / Num. obs: 27809 / % possible obs: 100 % / Redundancy: 17.6 % / Biso Wilson estimate: 30.81 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.017 / Rrim(I) all: 0.072 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.82→1.86 Å / Redundancy: 18 % / Rmerge(I) obs: 0.695 / Num. unique obs: 3136 / CC1/2: 0.973 / Rpim(I) all: 0.168 / Rrim(I) all: 0.715 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1bj1 Resolution: 2.3→85.65 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→85.65 Å
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Refine LS restraints |
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LS refinement shell |
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