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- PDB-3a2e: Crystal structure of ginkbilobin-2, the novel antifungal protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a2e | |||||||||
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Title | Crystal structure of ginkbilobin-2, the novel antifungal protein from Ginkgo biloba seeds | |||||||||
![]() | Ginkbilobin-2 | |||||||||
![]() | PLANT PROTEIN / DOMAIN 26 UNKNOWN FUNCTION (DUF26) / C-X8-C-X2-C MOTIF / ANTIFUNGAL PROTEIN / EMBRYO-ABUNDANT PROTEIN (EAP) | |||||||||
Function / homology | ![]() induction of programmed cell death / plasmodesma / aspartic-type endopeptidase inhibitor activity / D-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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Miyakawa, T. / Miyazono, K. / Sawano, Y. / Hatano, K. / Tanokura, M. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.9 KB | Display | ![]() |
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PDB format | ![]() | 80 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.8 KB | Display | ![]() |
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Full document | ![]() | 453.6 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11671.059 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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
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Refinement step | Cycle: LAST / Resolution: 2.38→43.17 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %
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