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Yorodumi- PDB-1xwv: Structure of the house dust mite allergen Der f 2: Implications f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xwv | ||||||
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Title | Structure of the house dust mite allergen Der f 2: Implications for function and molecular basis of IgE cross-reactivity | ||||||
Components | Der f II | ||||||
Keywords | ALLERGEN / BETA SHEETS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Dermatophagoides farinae (American house dust mite) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Johannessen, B.R. / Skov, L.K. / Kastrup, J.S. / Kristensen, O. / Bolwig, C. / Larsen, J.N. / Spangfort, M. / Lund, K. / Gajhede, M. | ||||||
Citation | Journal: Febs Lett. / Year: 2005 Title: Structure of the house dust mite allergen Der f 2: implications for function and molecular basis of IgE cross-reactivity. Authors: Johannessen, B.R. / Skov, L.K. / Kastrup, J.S. / Kristensen, O. / Bolwig, C. / Larsen, J.N. / Spangfort, M. / Lund, K. / Gajhede, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xwv.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xwv.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 1xwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/1xwv ftp://data.pdbj.org/pub/pdb/validation_reports/xw/1xwv | HTTPS FTP |
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-Related structure data
Related structure data | 1ktjS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14054.177 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dermatophagoides farinae (American house dust mite) Plasmid: pGAPZalpha-A / Production host: Pichia pastoris (fungus) / References: UniProt: Q00855 #2: Chemical | ChemComp-PE3 / | #3: Chemical | ChemComp-XPE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 4000, potassium citrate, ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→24.43 Å / Num. all: 18043 / Num. obs: 18043 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.83→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / Num. unique all: 2626 / Rsym value: 0.24 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KTJ Resolution: 1.83→24.43 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Displacement parameters | Biso mean: 30.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→24.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.94 Å / Rfactor Rfree error: 0.026
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