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Open data
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Basic information
Entry | Database: PDB / ID: 2ywy | ||||||
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Title | Structure of new antigen receptor variable domain from sharks | ||||||
![]() | new antigen receptor variable domain | ||||||
![]() | IMMUNE SYSTEM / IG VNAR / 1-A-7 | ||||||
Function / homology | ![]() Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Streltsov, V.A. | ||||||
![]() | ![]() Title: Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures Authors: Simmons, D.P. / Streltsov, V.A. / Dolezal, O. / Hudson, P.J. / Coley, A.M. / Foley, M. / Proll, D.F. / Nuttall, S.D. | ||||||
History |
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Remark 999 | SEQUENCE The sequence has been deposited to databasthe GB with accession code, DQ269922. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.8 KB | Display | ![]() |
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PDB format | ![]() | 78.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.3 KB | Display | ![]() |
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Full document | ![]() | 459.8 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ywzC ![]() 1vesS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12395.760 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pGC / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M ACETATE, 20% PEP (17/8 PO/OH), pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 2004 / Details: AXCO MICROCAPILLARY FOCUSING OPTICS |
Radiation | Monochromator: NO / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→21.57 Å / Num. obs: 19373 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.0119 / Rsym value: 0.0119 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.6 / % possible all: 87.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VES Resolution: 2.71→21.57 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.873 / SU B: 21.432 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.6 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→21.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.78 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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