+Open data
-Basic information
Entry | Database: PDB / ID: 3gnu | ||||||
---|---|---|---|---|---|---|---|
Title | Toxin fold as basis for microbial attack and plant defense | ||||||
Components | 25 kDa protein elicitor | ||||||
Keywords | TOXIN / phytopathogenic / oomycete | ||||||
Function / homology | : / Necrosis inducing protein / Necrosis inducing protein (NPP1) / metal ion binding / GUANIDINE / 25 kDa protein elicitor Function and homology information | ||||||
Biological species | Pythium aphanidermatum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gnu.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gnu.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gnu ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gnu | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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.) Pythium aphanidermatum (eukaryote) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9SPD4 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % |
---|---|
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 143611 / Rmerge(I) obs: 0.072 / D res high: 2.1 Å / Num. obs: 27871 / % possible obs: 99.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.9→24.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.161 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|