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- PDB-1xt5: Crystal Structure of VCBP3, domain 1, from Branchiostoma floridae -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xt5 | ||||||
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Title | Crystal Structure of VCBP3, domain 1, from Branchiostoma floridae | ||||||
![]() | variable region-containing chitin-binding protein 3 | ||||||
![]() | IMMUNE SYSTEM / innate immunity / vcbp / primordial antigen receptor / florida lancelet / amphioxus | ||||||
Function / homology | ![]() chitinase / chitinase activity / chitin binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hernandez Prada, J.A. / Haire, R.N. / Cannon, J.P. / Allaire, M. / Jakoncic, J. / Stojanoff, V. / Litman, G.W. / Ostrov, D.A. | ||||||
![]() | ![]() Title: Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus. Authors: Haire, R.N. / Allaire, M. / Jakoncic, J. / Stojanoff, V. / Cannon, J.P. / Litman, G.W. / Ostrov, D.A. #1: ![]() Title: Crystallization and preliminary X-ray analysis of VCBP3 from Branchiostoma floridae. Authors: Hernandez Prada, J.A. / Haire, R.N. / Cannon, J.P. / Litman, G.W. / Ostrov, D.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.4 KB | Display | ![]() |
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PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.3 KB | Display | ![]() |
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Full document | ![]() | 442.6 KB | Display | |
Data in XML | ![]() | 10.2 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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Unit cell |
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Components on special symmetry positions |
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Details | biological unit unknown |
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Components
#1: Protein | Mass: 14797.479 Da / Num. of mol.: 1 Fragment: sequence database residues 16-150: contains immunoglobulin like region (residues 33-146) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: VCBP3 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.708 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.2-1.4 M ammonium sulfate, 0.1 M NaCl, 0.1 M tris-HCl (or HEPES), 12% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2004 Details: Oxford Danfysik toroidal focusing mirror, Si(111) channel cut monochromator | |||||||||||||||
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.15→30 Å / Num. all: 57420 / Num. obs: 57420 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 59.3 | |||||||||||||||
Reflection shell | Resolution: 1.15→1.16 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 6 / Num. unique all: 1898 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ~3%.
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 904.7 / Occupancy sum non hydrogen: 1214.85 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→20 Å
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Refine LS restraints |
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LS refinement shell |
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