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Yorodumi- PDB-3ljd: The X-ray structure of zebrafish RNase1 from a new crystal form a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ljd | ||||||
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Title | The X-ray structure of zebrafish RNase1 from a new crystal form at pH 4.5 | ||||||
Components | Zebrafish RNase1 | ||||||
Keywords | HYDROLASE / angiogenins / fish rnases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Russo Krauss, I. / Merlino, A. / Mazzarella, L. / Sica, F. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish. Authors: Pizzo, E. / Merlino, A. / Turano, M. / Russo Krauss, I. / Coscia, F. / Zanfardino, A. / Varcamonti, M. / Furia, A. / Giancola, C. / Mazzarella, L. / Sica, F. / D'Alessio, G. #1: Journal: J.Biol.Chem. / Year: 2006 Title: Ribonucleases and angiogenins from fish Authors: Pizzo, E. / Buonanno, P. / DI Maro, A. / Ponticelli, S. / De Falco, S. / Quarto, N. / Cubellis, M.V. / D'Alessio, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ljd.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ljd.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 3ljd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ljd_validation.pdf.gz | 466.2 KB | Display | wwPDB validaton report |
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Full document | 3ljd_full_validation.pdf.gz | 475.4 KB | Display | |
Data in XML | 3ljd_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 3ljd_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/3ljd ftp://data.pdbj.org/pub/pdb/validation_reports/lj/3ljd | HTTPS FTP |
-Related structure data
Related structure data | 3ljeC 3ln8C 1agiS C: citing same article (ref.) 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14353.369 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Escherichia coli (E. coli) / References: UniProt: E7FH76*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / | #4: 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: 1.94 Å3/Da / Density % sol: 36.52 % |
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Crystal grow | Temperature: 293 K / pH: 4.5 Details: Drops were prepared by mixing equal volumes of protein solution (15 mg/ml) and reservoir solution (2M ammonium sulphate and 0.1M sodium acetate), pH 4.5, VAPOR DIFFUSION, HANGING 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 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2008 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→30 Å / Num. obs: 41877 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AGI Resolution: 1.38→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.38→30 Å
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Refine LS restraints |
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