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Yorodumi- PDB-1lp8: HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL PROTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lp8 | ||||||
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Title | HIGH RESOLUTION STRUCTURE OF RECOMBINANT DIANTHIN ANTIVIRAL PROTEIN-POTENT ANTI-HIV AGENT | ||||||
Components | DIANTHIN 30 | ||||||
Keywords | ANTIVIRAL PROTEIN / DIANTHIN ANTIVIRAL PROTEIN / RIBOSOME INACTIVATING PROTEIN / ANTI-HIV AGENT / HIV-1 INTEGRASE INHIBITOR / POLYNUCLEOTIDE:ADENOSINE GLYCOSIDASE | ||||||
Function / homology | Function and homology information 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 | Dianthus caryophyllus (clove pink) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Kurinov, I.V. / Rajamohan, F. / Uckun, F.M. | ||||||
Citation | Journal: Arzneimittelforschung / Year: 2004 Title: High resolution X-ray structure and potent anti-HIV activity of recombinant dianthin antiviral protein. Authors: Kurinov, I.V. / Rajamohan, F. / Uckun, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lp8.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lp8.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lp8_validation.pdf.gz | 360 KB | Display | wwPDB validaton report |
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Full document | 1lp8_full_validation.pdf.gz | 362.2 KB | Display | |
Data in XML | 1lp8_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1lp8_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lp8 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lp8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28603.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dianthus caryophyllus (clove pink) / Production host: Escherichia coli (E. coli) / References: UniProt: P24476, 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: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 26% PEG3350, 0.1M CaCl2, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 25, 2000 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 28432 / Num. obs: 26801 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.049 / Net I/σ(I): 46.9 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.107 / % possible all: 70.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HOMOLOGY MODELING Resolution: 1.65→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.5 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→8 Å
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Refine LS restraints |
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