[English] 日本語
![](img/lk-miru.gif)
- PDB-4bkc: Crystal Structure of a unusually linked dimeric variant of Bet v 1 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4bkc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of a unusually linked dimeric variant of Bet v 1 | |||||||||
![]() | MAJOR POLLEN ALLERGEN BET V 1-A | |||||||||
![]() | ALLERGEN / DIMERISATION / POLYSULFIDE / SULFUR INCORPORATION | |||||||||
Function / homology | ![]() response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kofler, S.G. / Brandstetter, H. | |||||||||
![]() | ![]() Title: Stabilization of the Dimeric Birch Pollen Allergen Bet V 1 Impacts its Immunological Properties Authors: Kofler, S.G. / Ackaert, C. / Samonig, M. / Asam, C. / Briza, P. / Horeis-Hoeck, J. / Cabrele, C. / Ferreira, F. / Duschl, A. / Huber, C. / Brandstetter, H. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 143.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 113.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 442.1 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bk6C ![]() 4bk7C ![]() 4bkdC ![]() 4a88S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17465.691 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: BOTH MONOMERS ARE LINKED VIA A POLYSULFIDE BRIDGE BETWEEN CYS5A AND CYS5B. DUE TO OCCUPANCY REASONS, THE MODIFIED CYSTEINE RESIDUES ARE INTRODUCED AS DISCRETE COMPOUNDS. Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.86 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 / Details: 0.1 M NA ACETATE PH 6.5, 27 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8865 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→41.62 Å / Num. obs: 38874 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.5 / % possible all: 98 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4A88 Resolution: 1.73→56.97 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.534 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY THE LIGANDS INCLUDED IN THE STRUCTURE ARE CYSTEINES BOUND TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY THE LIGANDS INCLUDED IN THE STRUCTURE ARE CYSTEINES BOUND TO ADDITIONAL CYSTEINES, AND ACCORDINGLY CYSTINE LINKED VIA 4 SULFUR ATOMS. THESE LIGANDS ARE POSITIONED AT THE SAME SITE AS CYS5 AND THEREFORE CAN BE CONSIDERED AS ALTERNATIVE CONFORMATIONS. THIS IS REFLECTED BY THE OCCUPANCIES OF THE ATOMS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.962 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→56.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|