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- PDB-7sbg: Murine Fab/IgE in complex with profilin from Hevea brasieliensis ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sbg | ||||||
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Title | Murine Fab/IgE in complex with profilin from Hevea brasieliensis (Hev b 8) | ||||||
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![]() | ALLERGEN/IMMUNE SYSTEM / ![]() ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rodriguez-Romero, A. / Garcia-Ramirez, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A native IgE in complex with profilin provides insights into allergen recognition and cross-reactivity. Authors: Garcia-Ramirez, B. / Mares-Mejia, I. / Rodriguez-Hernandez, A. / Cano-Sanchez, P. / Torres-Larios, A. / Ortega, E. / Rodriguez-Romero, A. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2006 Title: HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes. Authors: Minor, W. / Cymborowski, M. / Otwinowski, Z. / Chruszcz, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.5 KB | Display | ![]() |
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PDB format | ![]() | 82.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sbdSC ![]() 7sd2C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Antibody | Mass: 23226.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23616.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#3: Protein | ![]() Mass: 14636.482 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.3 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 0.2 M lithium acetate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.23→40.22 Å / Num. obs: 7675 / % possible obs: 98.85 % / Redundancy: 1.8 % / Biso Wilson estimate: 89.28 Å2 / CC1/2: 0.993 / Net I/σ(I): 16.65 |
Reflection shell | Resolution: 3.23→3.35 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.432 / Num. unique obs: 749 / CC1/2: 0.67 / % possible all: 91.89 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 7SBD Resolution: 3.34→37.57 Å / SU ML: 0.5174 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8135 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.34→37.57 Å
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Refine LS restraints |
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LS refinement shell |
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