+Open data
-Basic information
Entry | Database: PDB / ID: 2a8f | ||||||
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Title | beta-cinnamomin after sterol removal | ||||||
Components | Beta-elicitin cinnamomin | ||||||
Keywords | TOXIN / elicitin / sterol carrier protein / phytophthora / phytopathogen | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host defense-related programmed cell death / symbiont-mediated killing of host cell / lipid transport / steroid binding / extracellular region Similarity search - Function | ||||||
Biological species | Phytophthora cinnamomi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Rodrigues, M.L. / Archer, M. / Martel, P. / Miranda, S. / Thomaz, M. / Enguita, F.J. / Baptista, R.P. / Melo, E.P. / Sousa, N. / Cravador, A. / Carrondo, M.A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2006 Title: Crystal structures of the free and sterol-bound forms of beta-cinnamomin Authors: Rodrigues, M.L. / Archer, M. / Martel, P. / Miranda, S. / Thomaz, M. / Enguita, F.J. / Baptista, R.P. / Melo, E.P. / Sousa, N. / Cravador, A. / Carrondo, M.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structure of beta-cinnamomin, a protein toxic to some plant species. Authors: Rodrigues, M.L. / Archer, M. / Martel, P. / Jacquet, A. / Cravador, A. / Carrondo, M.A. #2: Journal: DNA Seq. / Year: 1998 Title: Identification of an elicitin gene cluster in Phytophthora cinnamomi. Authors: Duclos, J. / Fauconnier, A. / Coelho, A.C. / Bollen, A. / Cravador, A. / Godfroid, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a8f.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a8f.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 2a8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/2a8f ftp://data.pdbj.org/pub/pdb/validation_reports/a8/2a8f | HTTPS FTP |
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-Related structure data
Related structure data | 2aibC 1ljpS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 10299.760 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora cinnamomi (eukaryote) / Gene: CIN1B / Plasmid: pIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1168 / References: UniProt: P15569 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 4000, Hepes buffer, MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50.99 Å / Num. all: 39554 / Num. obs: 39554 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.35→1.38 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LJP Resolution: 1.35→50.99 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→50.99 Å
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Refine LS restraints |
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