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Open data
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Basic information
Entry | Database: PDB / ID: 3gnu | ||||||
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Title | Toxin fold as basis for microbial attack and plant defense | ||||||
![]() | 25 kDa protein elicitor | ||||||
![]() | TOXIN / phytopathogenic / oomycete | ||||||
Function / homology | Necrosis inducing protein / Necrosis inducing protein (NPP1) / killing of cells of another organism / metal ion binding / GUANIDINE / 25 kDa protein elicitor![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ottmann, C. / Luberacki, B. / Kuefner, I. / Koch, W. / Brunner, F. / Weyand, M. / Mattinen, L. / Pirhonen, M. / Anderluh, G. / Seitz, H.U. ...Ottmann, C. / Luberacki, B. / Kuefner, I. / Koch, W. / Brunner, F. / Weyand, M. / Mattinen, L. / Pirhonen, M. / Anderluh, G. / Seitz, H.U. / Nuernberger, T. / Oecking, C. | ||||||
![]() | ![]() Title: A common toxin fold mediates microbial attack and plant defense Authors: Ottmann, C. / Luberacki, B. / Kufner, I. / Koch, W. / Brunner, F. / Weyand, M. / Mattinen, L. / Pirhonen, M. / Anderluh, G. / Seitz, H.U. / Nurnberger, T. / Oecking, C. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Purification, crystallization and preliminary X-ray diffraction analysis of an oomycete-derived Nep1-like protein. Authors: Luberacki, B. / Weyand, M. / Seitz, U. / Koch, W. / Oecking, C. / Ottmann, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.5 KB | Display | ![]() |
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PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.9 KB | Display | ![]() |
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Full document | ![]() | 438.4 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 23359.971 Da / Num. of mol.: 1 / Fragment: UNP residues 22-234 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M HEPES-NaOH, 5.0M NaCl, 2% DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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 | Number: 143611 / Rmerge(I) obs: 0.072 / D res high: 2.1 Å / Num. obs: 27871 / % possible obs: 99.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.9→25 Å / Num. all: 19827 / Num. obs: 19306 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 25.481 Å2 / Rmerge(I) obs: 0.044 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.7 / Num. measured obs: 10994 / Num. unique all: 2501 / Num. unique obs: 2501 / Rsym value: 0.331 / % possible all: 90.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 max: 54.39 Å2 / Biso mean: 20.16 Å2 / Biso min: 7.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.195 Å / Luzzati d res low obs: 7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→24.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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