+Open data
-Basic information
Entry | Database: PDB / ID: 4wfv | ||||||
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Title | Bovine allergen Bos d 2 in the monoclinic space group C2. | ||||||
Components | Allergen Bos d 2 | ||||||
Keywords | ALLERGEN / lipocalin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Niemi, M.H. / Rouvinen, J. | ||||||
Funding support | Finland, 1items
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Citation | Journal: Sci Rep / Year: 2015 Title: Dimerization of lipocalin allergens. Authors: Niemi, M.H. / Rytkonen-Nissinen, M. / Miettinen, I. / Janis, J. / Virtanen, T. / Rouvinen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wfv.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wfv.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/4wfv ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wfv | HTTPS FTP |
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-Related structure data
Related structure data | 4wfuC 1bj7S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 17867.984 Da / Num. of mol.: 1 / Fragment: UNP Residues 17-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q28133 |
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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: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 2.5 M 1,6-hexanediol, 0.1 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.011 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.011 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 31792 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 12.02 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.037 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.2 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BJ7 Resolution: 1.4→25.603 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.937 Å2 / ksol: 0.476 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.47 Å2 / Biso mean: 14.0511 Å2 / Biso min: 4.56 Å2
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Refinement step | Cycle: final / Resolution: 1.4→25.603 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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