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Yorodumi- PDB-2i24: Crystal structure analysis of the nurse shark New Antigen Recepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i24 | ||||||
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Title | Crystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domain | ||||||
Components | New Antigen Receptor PBLA8 | ||||||
Keywords | IMMUNE SYSTEM / immunoglobulin fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ginglymostoma cirratum (nurse shark) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Stanfield, R.L. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 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 PBLA8. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i24.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i24.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 2i24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i24_validation.pdf.gz | 389.1 KB | Display | wwPDB validaton report |
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Full document | 2i24_full_validation.pdf.gz | 389.1 KB | Display | |
Data in XML | 2i24_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 2i24_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/2i24 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/2i24 | HTTPS FTP |
-Related structure data
Related structure data | 2i25C 2i26C 2i27C 1sq2S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 13437.806 Da / Num. of mol.: 1 / Fragment: variable domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Plasmid: pims100 / Production host: Escherichia coli (E. coli) / Strain (production host): xl1-blue / References: UniProt: Q8AXH5 |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 24% PEG 400, 0.1M Na/K phosphate, 0.15M NaCl, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97623 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→44.7 Å / Num. all: 26060 / Num. obs: 26060 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.056 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 1.95 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1226 / Rsym value: 0.46 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SQ2, CHAIN N Resolution: 1.35→44.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.008 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.061 / ESU R Free: 0.06 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.858 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→44.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 30.9152 Å / Origin y: 4.6679 Å / Origin z: 61.9594 Å
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