+Open data
-Basic information
Entry | Database: PDB / ID: 1ver | ||||||
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Title | Structure of New Antigen Receptor variable domain from sharks | ||||||
Components | New Antigen Receptor variable domain | ||||||
Keywords | IMMUNE SYSTEM / IG VNAR / NATIVE / 12Y-1 | ||||||
Function / homology | Function and homology information 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 | Orectolobus maculatus (spotted wobbegong) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.82 Å | ||||||
Authors | Streltsov, V.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor Authors: Streltsov, V.A. / Varghese, J.N. / Carmichael, J.A. / Irving, R.A. / Hudson, P.J. / Nuttall, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ver.cif.gz | 33.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ver.ent.gz | 23.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ver.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1ver ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1ver | HTTPS FTP |
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-Related 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: 12266.757 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Orectolobus maculatus (spotted wobbegong) Plasmid: pGC / Production host: Escherichia coli (E. coli) / References: UniProt: Q6X1E7 |
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#2: 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: 3.14 Å3/Da / Density % sol: 60.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M BIS-TRIS PROPANE, 45% PPG P400, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2003 / Details: Axco microcapillary focusing optics |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→69.01 Å / Num. obs: 3975 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.82→2.9 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.8 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.82→6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.179 / SU ML: 0.288 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 40.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.82→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.82→2.877 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 45.611 Å / Origin y: 36.411 Å / Origin z: 14.235 Å
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