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Yorodumi- PDB-2g5x: Crystal structure of lychnin a type 1 Ribosome Inactivating Prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g5x | ||||||
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Title | Crystal structure of lychnin a type 1 Ribosome Inactivating Protein (RIP) | ||||||
Components | Ribosome-inactivating protein | ||||||
Keywords | HYDROLASE / alpha-beta protein | ||||||
Function / homology | Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | Lychnis chalcedonica (scarlet lychnis) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Fermani, S. / Falini, G. / Tosi, G. / Ripamonti, A. / Polito, L. / Bolognesi, A. / Stirpe, F. | ||||||
Citation | Journal: To be Published Title: Crystal structure of lychnin a type 1 Ribosome Inactivating Protein (RIP) Authors: Fermani, S. / Falini, G. / Tosi, G. / Ripamonti, A. / Polito, L. / Bolognesi, A. / Stirpe, F. #1: Journal: Biochim.Biophys.Acta / Year: 1990 Title: Purification and properties of new ribosome-inactivating proteins with RNA N-glycosidase activity Authors: Bolognesi, A. / Barbieri, L. / Abbondanza, A. / Falasca, A.I. / Carnicelli, D. / Battelli, M.G. / Stirpe, F. #2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003 Title: Crystallization and preliminary X-ray diffraction analysis of two ribosome-inactivating proteins: lychnin and dianthin 30 Authors: Fermani, S. / Falini, G. / Ripamonti, A. / Bolognesi, A. / Polito, L. / Stirpe, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g5x.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g5x.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 2g5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/2g5x ftp://data.pdbj.org/pub/pdb/validation_reports/g5/2g5x | HTTPS FTP |
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-Related structure data
Related structure data | 1wuc 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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Details | The protein is a monomer. The asymmetric unit contain one monomer |
-Components
#1: Protein | Mass: 26163.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lychnis chalcedonica (scarlet lychnis) / Tissue: seedsSeed / References: rRNA N-glycosylase |
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#2: 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: 1.97 Å3/Da / Density % sol: 37.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG 8000, 0.1M sodium phosphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 17, 2002 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.1 Å / Num. all: 22021 / Num. obs: 21895 / % possible obs: 51 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.048 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 14.2 / Num. unique all: 2162 / Rsym value: 0.084 / % possible all: 50.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WUC 1wuc Resolution: 1.7→28.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 948638.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80.4733 Å2 / ksol: 0.460368 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→28.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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