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Yorodumi- PDB-5ev0: Crystal structure of ragweed profilin Amb a 8 in complex with pol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ev0 | ||||||
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Title | Crystal structure of ragweed profilin Amb a 8 in complex with poly-Pro14 | ||||||
Components |
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Keywords | ALLERGEN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ambrosia artemisiifolia (common ragweed) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Offermann, L.R. / He, J.Z. / Perdue, M.L. / Chruszcz, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural, Functional, and Immunological Characterization of Profilin Panallergens Amb a 8, Art v 4, and Bet v 2. Authors: Offermann, L.R. / Schlachter, C.R. / Perdue, M.L. / Majorek, K.A. / He, J.Z. / Booth, W.T. / Garrett, J. / Kowal, K. / Chruszcz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ev0.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ev0.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 5ev0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/5ev0 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/5ev0 | HTTPS FTP |
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-Related structure data
Related structure data | 5em0SC 5em1C 5eveC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 14346.314 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ambrosia artemisiifolia (common ragweed) Plasmid: pJExpress411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2KN24 #2: Protein/peptide | Mass: 892.048 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: 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: 2.13 Å3/Da / Density % sol: 42.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M HEPES, pH 6.5, 1.4 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 14967 / Num. obs: 14967 / % possible obs: 98.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.7 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5EM0 Resolution: 2.1→45.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.784 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.94 Å2 / Biso mean: 35.564 Å2 / Biso min: 18.91 Å2
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Refinement step | Cycle: final / Resolution: 2.1→45.47 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 7256 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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