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Yorodumi- PDB-1zld: Crystal structure of a RGD-containing host-selective toxin: Pyren... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zld | |||||||||
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Title | Crystal structure of a RGD-containing host-selective toxin: Pyrenophora tritici-repentis Ptr ToxA | |||||||||
Components | Ptr necrosis toxin | |||||||||
Keywords | TOXIN / beta-sandwich / RGD-motif | |||||||||
Function / homology | Proteinaceous host-selective toxin ToxA / Proteinaceous host-selective toxin ToxA / ToxA superfamily / Proteinaceous host-selective toxin ToxA / Immunoglobulin-like / Sandwich / Mainly Beta / A necrosis toxin Function and homology information | |||||||||
Biological species | Pyrenophora tritici-repentis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | |||||||||
Authors | Sarma, G.N. / Manning, V.A. / Ciuffetti, L.M. / Karplus, P.A. | |||||||||
Citation | Journal: Plant Cell / Year: 2005 Title: Structure of Ptr ToxA: An RGD-Containing Host-Selective Toxin from Pyrenophora tritici-repentis Authors: Sarma, G.N. / Manning, V.A. / Ciuffetti, L.M. / Karplus, P.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zld.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zld.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/1zld ftp://data.pdbj.org/pub/pdb/validation_reports/zl/1zld | HTTPS FTP |
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-Related 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: 13207.755 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Source method: isolated from a natural source / Source: (natural) Pyrenophora tritici-repentis (fungus) / References: UniProt: P78737 | ||
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#2: Chemical | #3: 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 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.5 M Ammonium sulfate, 15% Dioxane, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 15, 2004 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 19466 / Num. obs: 19466 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 4.7 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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