+Open data
-Basic information
Entry | Database: PDB / ID: 1fm4 | ||||||
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Title | CRYSTAL STRUCTURE OF THE BIRCH POLLEN ALLERGEN BET V 1L | ||||||
Components | MAJOR POLLEN ALLERGEN BET V 1-L | ||||||
Keywords | ALLERGEN / alpha-beta: 6 anti-parallel beta strands and 3 alpha helices. | ||||||
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 / Resolution: 1.97 Å | ||||||
Authors | Markovic-Housley, Z. / Degano, M. / Lamba, D. / von Roepenack-Lahaye, E. / Clemens, S. / Susani, M. / Ferreira, F. / Scheiner, O. / Breiteneder, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of a Hypoallergenic Isoform of the Major Birch Pollen Allergen Bet v 1 and its Likely Biological Function as a Plant Steroid Carrier Authors: Markovic-Housley, Z. / Degano, M. / Lamba, D. / von Roepenack-Lahaye, E. / Clemens, S. / Susani, M. / Ferreira, F. / Scheiner, O. / Breiteneder, H. #1: Journal: J.Biol.Chem. / Year: 1995 Title: Isoforms of Bet v 1, the major birch pollen allergen, analyzed by liquid chromatography, mass spectrometry, and cDNA cloning. Authors: Swoboda, I. / Jilek, A. / Ferreira, F. / Engel, E. / Hoffman-Sommergruber, K. / Scheiner, O. / Kraft, D. / Breiteneder, H. / Pittenauer, E. / Schmid, E. / Vicente, O. / Heberle-Bors, E. / ...Authors: Swoboda, I. / Jilek, A. / Ferreira, F. / Engel, E. / Hoffman-Sommergruber, K. / Scheiner, O. / Kraft, D. / Breiteneder, H. / Pittenauer, E. / Schmid, E. / Vicente, O. / Heberle-Bors, E. / Ahorn, H. / Breitenbach, M. #2: Journal: Embo J. / Year: 1989 Title: The gene coding for the major birch pollen allergen Betv1, is highly homologous to a pea disease resistance response gene. Authors: Breiteneder, H. / Pettenburger, K. / Bito, A. / Valenta, R. / Kraft, D. / Rumpold, H. / Scheiner, O. / Breitenbach, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fm4.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fm4.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fm4_validation.pdf.gz | 948.5 KB | Display | wwPDB validaton report |
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Full document | 1fm4_full_validation.pdf.gz | 951.9 KB | Display | |
Data in XML | 1fm4_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1fm4_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/1fm4 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/1fm4 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 17430.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Betula pendula (European white birch) / Tissue: POLLEN / Plasmid: PMW 175-BET V 1L / Production host: Escherichia coli (E. coli) / References: UniProt: P43185 | ||
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#2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 41.43 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100mM sodium acetate, 20mM ammonium sulphate, 30%Peg-MME 2000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→30 Å / Num. all: 32201 / Num. obs: 9670 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.3 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.97→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.371 / Num. unique all: 607 / % possible all: 59.6 |
Reflection | *PLUS Num. measured all: 32201 |
Reflection shell | *PLUS % possible obs: 59.6 % / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Resolution: 1.97→28.66 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 807800.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent correction
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.13 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.97→28.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / σ(I): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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