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Yorodumi- PDB-4a80: Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a80 | ||||||
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Title | Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with 8-Anilinonaphthalene-1-sulfonate (ANS) | ||||||
Components | MAJOR POLLEN ALLERGEN BET V 1-A | ||||||
Keywords | ALLERGEN / PR-10 PROTEIN | ||||||
Function / homology | Function and homology information response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / cytoplasm Similarity search - Function | ||||||
Biological species | BETULA PENDULA (European white birch) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Kofler, S. / Brandstetter, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Crystallographically Mapped Ligand Binding Differs in High and Low Ige Binding Isoforms of Birch Pollen Allergen Bet V 1. Authors: Kofler, S. / Asam, C. / Eckhard, U. / Wallner, M. / Ferreira, F. / Brandstetter, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a80.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a80.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 4a80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/4a80 ftp://data.pdbj.org/pub/pdb/validation_reports/a8/4a80 | HTTPS FTP |
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-Related structure data
Related structure data | 4a81C 4a83C 4a84C 4a85C 4a86C 4a87C 4a88C 4a8gC 4a8uC 4a8vC 1fm4S C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 17461.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BETULA PENDULA (European white birch) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15494 | ||||
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#2: Chemical | ChemComp-2AN / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | THE UNIPROT SEQUENCE IS FURTHER PROCESSED INTO A MATURE FORM. MATURE PROTEIN HAS STARTING METHIONINE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.49 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→37.88 Å / Num. obs: 8488 / % possible obs: 90.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.13 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 21.8 / % possible all: 98.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FM4 Resolution: 1.96→37.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.383 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUE REFINED INDIVIDUALLY. RESIDUES 124-126 LACK WELL DEFINED BACKBONE DENSITY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.387 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→37.88 Å
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