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Open data
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Basic information
Entry | Database: PDB / ID: 2f08 | ||||||
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Title | Crystal structure of a major house dust mite allergen, Derf 2 | ||||||
![]() | mite allergen Der f II | ||||||
![]() | IMMUNE SYSTEM / immunoglobulin fold | ||||||
Function / homology | ![]() intracellular cholesterol transport / cholesterol efflux / cholesterol binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mikami, B. / Tanaka, Y. / Minato, N. / Suzuki, M. / Korematsu, S. | ||||||
![]() | ![]() Title: Crystal structure and some properties of a major house dust mite allergen, Derf 2 Authors: Suzuki, M. / Tanaka, Y. / Korematsu, S. / Mikami, B. / Minato, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.3 KB | Display | ![]() |
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PDB format | ![]() | 88.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 695.7 KB | Display | ![]() |
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Full document | ![]() | 708.1 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | The biological assembly is a monomer. |
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Components
#1: Protein | Mass: 14064.193 Da / Num. of mol.: 4 / Fragment: residues 1-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-P4C / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 23% PEG 4000, 0.06M ammonium sulfate, 0.1M sodium acetate, 10mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Dec 21, 1999 / Details: carbon monochrometer |
Radiation | Monochromator: carbon monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→28.3 Å / Num. all: 34340 / Num. obs: 32658 / % possible obs: 95.05 % / Observed criterion σ(I): 1 / Redundancy: 3.38 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.058 / Net I/σ(I): 25.83 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 3.37 % / Mean I/σ(I) obs: 2.61 / Num. unique all: 3009 / Rsym value: 0.342 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.6915 Å2 / ksol: 0.259142 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→14.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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