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Yorodumi- PDB-1o9f: Structural view of a fungal toxin acting on a 14-3-3 regulatory c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o9f | ||||||
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Title | Structural view of a fungal toxin acting on a 14-3-3 regulatory complex | ||||||
Components |
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Keywords | PROTEIN BINDING / PROTEIN-BINDING / FUSICOCCIN / 14-3-3 FAMILY / ACTIVATING DRUG / PLANT PLASMA MEMBRANE (H+)ATPASE | ||||||
Function / homology | Function and homology information P-type proton-exporting transporter activity / regulation of intracellular pH / protein localization / signal transduction / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | NICOTIANA TABACUM (common tobacco) NICOTIANA PLUMBAGINIFOLIA (curled-leaved tobacco) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Wurtele, M. / Jelich-Ottmann, C. / Wittinghofer, A. / Oecking, C. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Structural View of a Fungal Toxin Acting on a 14-3-3 Regulatory Complex Authors: Wurtele, M. / Jelich-Ottmann, C. / Wittinghofer, A. / Oecking, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o9f.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o9f.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 1o9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o9f_validation.pdf.gz | 813 KB | Display | wwPDB validaton report |
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Full document | 1o9f_full_validation.pdf.gz | 819 KB | Display | |
Data in XML | 1o9f_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 1o9f_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o9f ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o9f | HTTPS FTP |
-Related structure data
Related structure data | 1o9cC 1o9dC 1o9eC 1a4oS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | THE ENTRY IS A DIMER OF CHAIN A, WHICH BECOMES A TETRAMER AS PEPTIDE CHAIN P IS IN COMPLEX WITH CHAIN A. |
-Components
#1: Protein | Mass: 29399.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GENE BANK AAC49892 / Source: (gene. exp.) NICOTIANA TABACUM (common tobacco) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P93343 |
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#2: Protein/peptide | Mass: 676.610 Da / Num. of mol.: 1 / Fragment: RESIDUES 436-440 / Source method: obtained synthetically Source: (synth.) NICOTIANA PLUMBAGINIFOLIA (curled-leaved tobacco) References: UniProt: Q40409 |
#3: Chemical | ChemComp-FSC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.09 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.4 / Details: PEG400, CITRAT PH 4.7, 0.2 MM AMMONIUM ACETATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Date: Dec 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→10 Å / Num. obs: 13170 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.2 / % possible all: 97.2 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 56531 |
Reflection shell | *PLUS % possible obs: 97.2 % / Rmerge(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A4O Resolution: 2.7→19.21 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 541374.11 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.7886 Å2 / ksol: 0.352667 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 5
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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