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Yorodumi- PDB-3ln8: The X-ray structure of Zf-RNase-1 from a new crystal form at pH 7.3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ln8 | ||||||
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Title | The X-ray structure of Zf-RNase-1 from a new crystal form at pH 7.3 | ||||||
Components | HYDROLASE | ||||||
Keywords | HYDROLASE / angiogenins / fish rnases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Danio Rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 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. #2: Journal: Gene / Year: 2007 Title: The success of the RNase scaffold in the advance of biosciences and in evolution Authors: Pizzo, E. / 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 | 3ln8.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ln8.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ln8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ln8_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 3ln8_full_validation.pdf.gz | 456.8 KB | Display | |
Data in XML | 3ln8_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3ln8_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/3ln8 ftp://data.pdbj.org/pub/pdb/validation_reports/ln/3ln8 | HTTPS FTP |
-Related structure data
Related structure data | 3ljdSC 3ljeC S: Starting model for refinement C: citing same article (ref.) |
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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: 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: 1.96 Å3/Da / Density % sol: 37.36 % |
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Crystal grow | Temperature: 293 K / pH: 7.3 Details: 2.0 M ammonium sulphate, 0.1 M TRIS/acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 9, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→30 Å / Num. obs: 28093 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.61→1.67 Å / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LJD Resolution: 1.61→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.61→30 Å
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Refine LS restraints |
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