[English] 日本語
Yorodumi- PDB-3a2e: Crystal structure of ginkbilobin-2, the novel antifungal protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a2e | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of ginkbilobin-2, the novel antifungal protein from Ginkgo biloba seeds | |||||||||
Components | Ginkbilobin-2 | |||||||||
Keywords | PLANT PROTEIN / DOMAIN 26 UNKNOWN FUNCTION (DUF26) / C-X8-C-X2-C MOTIF / ANTIFUNGAL PROTEIN / EMBRYO-ABUNDANT PROTEIN (EAP) | |||||||||
Function / homology | Function and homology information induction of programmed cell death / aspartic-type endopeptidase inhibitor activity / mannose binding / defense response to fungus / actin binding / killing of cells of another organism / defense response to bacterium / extracellular space Similarity search - Function | |||||||||
Biological species | Ginkgo biloba (maidenhair tree) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å | |||||||||
Authors | Miyakawa, T. / Miyazono, K. / Sawano, Y. / Hatano, K. / Tanokura, M. | |||||||||
Citation | Journal: Proteins / Year: 2009 Title: Crystal structure of ginkbilobin-2 with homology to the extracellular domain of plant cysteine-rich receptor-like kinases Authors: Miyakawa, T. / Miyazono, K. / Sawano, Y. / Hatano, K. / Tanokura, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3a2e.cif.gz | 96.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3a2e.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 3a2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/3a2e ftp://data.pdbj.org/pub/pdb/validation_reports/a2/3a2e | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
4 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 11671.059 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ginkgo biloba (maidenhair tree) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4ZDL6 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow |
|
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector |
| |||||||||||||||
Radiation |
| |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection twin | Operator: l,-k,h / Fraction: 0.485 | |||||||||||||||
Reflection | Resolution: 2.38→50 Å / Num. obs: 39529 / % possible obs: 99.7 % / Redundancy: 15.2 % / Rsym value: 0.061 / Net I/σ(I): 61.2 / Num. measured all: 602150 | |||||||||||||||
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 8.2 / Rsym value: 0.375 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.38→43.17 Å / Occupancy max: 1 / Occupancy min: 0.98 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.09 / Stereochemistry target values: TWIN_LSQ_F
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 87.147 Å2 / ksol: 0.346 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.92 Å2 / Biso mean: 34.8 Å2 / Biso min: 25.03 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→43.17 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %
|