[English] 日本語
Yorodumi- PDB-2rkn: X-ray structure of the self-defense and signaling protein DIR1 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rkn | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis taliana | ||||||
Components | DIR1 protein | ||||||
Keywords | SIGNALING PROTEIN / LIPID TRANSPORT / LTP / DEFENSE SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information secretory vesicle / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / plasmodesma / apoplast / lipid transport / fatty acid binding / : / endoplasmic reticulum / zinc ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Lascombe, M.B. / Prange, T. / Buhot, N. / Marion, D. / Bakan, B. / Lamb, C. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: The structure of "defective in induced resistance" protein of Arabidopsis thaliana, DIR1, reveals a new type of lipid transfer protein. Authors: Lascombe, M.B. / Bakan, B. / Buhot, N. / Marion, D. / Blein, J.P. / Larue, V. / Lamb, C. / Prange, T. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006 Title: Crystallization of DIR1, a LTP2-like resistance signalling protein from Arabidopsis thaliana Authors: Lascombe, M.B. / Buhot, N. / Bakan, B. / Marion, D. / Blein, J.P. / Lamb, C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2rkn.cif.gz | 31.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2rkn.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 2rkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/2rkn ftp://data.pdbj.org/pub/pdb/validation_reports/rk/2rkn | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8050.096 Da / Num. of mol.: 1 / Fragment: LTP DEFENSE PROTEIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DIR1 / Plasmid: pPICZalpha / Production host: pichia pastoris (fungus) / References: UniProt: Q8W453 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.31 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.08M acetate buffer pH 6.0, 0.02M ZnSO4, 22% PEG 600 MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Lowest resolution: 15 Å / Num. obs: 10412 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 31.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.82→1.92 Å / % possible all: 100 |
-Phasing
Phasing | Method: MAD |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.6→9.92 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.206 / SU B: 3.614 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.162 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→9.92 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 13.741 Å / Origin y: 5.349 Å / Origin z: 8.273 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|