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- PDB-1rl0: Crystal structure of a new ribosome-inactivating protein (RIP): d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rl0 | ||||||
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Title | Crystal structure of a new ribosome-inactivating protein (RIP): dianthin 30 | ||||||
![]() | Antiviral protein DAP-30 | ||||||
![]() | HYDROLASE / PLANT PROTEIN / mixed beta-sheet / alpha and beta regions | ||||||
Function / homology | ![]() regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fermani, S. / Falini, G. / Ripamonti, A. / Bolognesi, A. / Polito, L. / Stirpe, F. | ||||||
![]() | ![]() Title: The 1.4A structure of dianthin 30 indicates a role of surface potential at the active site of type 1 ribosome inactivating proteins Authors: Fermani, S. / Falini, G. / Ripamonti, A. / Polito, L. / Stirpe, F. / Bolognesi, A. #1: ![]() Title: Crystallization and preliminary X-ray diffraction analysis of two ribosomes-inactivating proteins: lychnin and dianthin 30 Authors: Fermani, S. / Falini, G. / Ripamonti, A. / Bolognesi, A. / Polito, L. / Stirpe, F. #2: ![]() Title: Ribosome-inactivating proteins from plants Authors: Barbieri, L. / Battelli, M.G. / Stirpe, F. #3: ![]() Title: Dianthins, ribosome-damaging proteins with anti-viral properties from Dianthus caryophyllus L. (carnation) Authors: Stirpe, F. / Williams, D.G. / Onyon, L.G. / Legg, R.F. / Stevens, W.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.1 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.2 KB | Display | ![]() |
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Full document | ![]() | 420.4 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qi7S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The protein is a monomeric enzyme, the asymmetric unit contains a single chain. |
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Components
#1: Protein | Mass: 28632.631 Da / Num. of mol.: 1 / Fragment: residues 24-278 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 28 % |
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Crystal grow | Temperature: 293 K / pH: 4.5 Details: PEG 4000, ammonium acetate, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 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: 1.4→39 Å / Num. obs: 44547 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 13.1 Å2 / Rsym value: 0.063 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.4→1.45 Å / Mean I/σ(I) obs: 10.4 / Rsym value: 0.255 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PBD ENTRY 1QI7 Resolution: 1.4→36.22 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 916080.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 78.95 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→36.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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