+Open data
-Basic information
Entry | Database: PDB / ID: 2otw | ||||||
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Title | Crystal structure of Fv polyglutamine complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / polyglutamine / complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å | ||||||
Authors | Li, P. | ||||||
Citation | Journal: To be Published Title: Implications of the structure of a poly-Gln/anti-poly-Gln complex for disease progression and therapy Authors: Li, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2otw.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2otw.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 2otw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2otw_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 2otw_full_validation.pdf.gz | 481.9 KB | Display | |
Data in XML | 2otw_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 2otw_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/2otw ftp://data.pdbj.org/pub/pdb/validation_reports/ot/2otw | HTTPS FTP |
-Related structure data
Related structure data | 2otuC 2gsgS 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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2 |
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Unit cell |
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Details | Each antibody/antigen complex contains VH, VL and Peptide |
-Components
#1: Antibody | Mass: 12460.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: VL / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Antibody | Mass: 13330.936 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: VH / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #3: Protein/peptide | Mass: 1413.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.84 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.5 Details: 0.1 M sodium citrate, 0.2 M NH4Ac, 27.5% PEG400, pH 6.5, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006 / Details: Si (111) crystal |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 28033 / Num. obs: 27313 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.052 / Rsym value: 5.2 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2243 / Rsym value: 22.1 / % possible all: 81.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 2GSG Resolution: 2.35→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.35→50 Å
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Refine LS restraints |
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