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- PDB-2i27: Crystal Structure Analysis of the Nurse Shark New Antigen Recepto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2i27 | ||||||
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Title | Crystal Structure Analysis of the Nurse Shark New Antigen Receptor Ancestral variable domain | ||||||
![]() | New Antigen Receptor Ancestral | ||||||
![]() | IMMUNE SYSTEM / immunoglobulin fold | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Stanfield, R.L. / Wilson, I.A. | ||||||
![]() | ![]() Title: Maturation of Shark Single-domain (IgNAR) Antibodies: Evidence for Induced-fit Binding. Authors: Stanfield, R.L. / Dooley, H. / Verdino, P. / Flajnik, M.F. / Wilson, I.A. | ||||||
History |
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Remark 999 | SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR THE NEW ANTIGEN ...SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR THE NEW ANTIGEN RECEPTOR ANCESTRAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.8 KB | Display | ![]() |
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PDB format | ![]() | 40.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.3 KB | Display | ![]() |
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Full document | ![]() | 437.9 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13294.453 Da / Num. of mol.: 2 / Fragment: variable domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 26% PEG 4000, 0.1M hepes, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979454 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. all: 15147 / Num. obs: 15147 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.09 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 5075 / Rsym value: 0.664 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.543 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 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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