+Open data
-Basic information
Entry | Database: PDB / ID: 3lje | ||||||
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Title | The X-ray structure of zebrafish RNase5 | ||||||
Components | Zebrafish RNase5 | ||||||
Keywords | HYDROLASE / angiogenins / fish rnases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Russo Krauss, I. / Merlino, A. / Coscia, F. / 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: Gene / Year: 2007 Title: The success of the RNase scaffold in the advance of bioscience and in evolution. Authors: Pizzo, E. / D'Alessio, G. #2: 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 | 3lje.cif.gz | 41.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lje.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lje_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 3lje_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 3lje_validation.xml.gz | 9 KB | Display | |
Data in CIF | 3lje_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/3lje ftp://data.pdbj.org/pub/pdb/validation_reports/lj/3lje | HTTPS FTP |
-Related structure data
Related structure data | 3ljdSC 3ln8C 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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Unit cell |
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-Components
#1: Protein | Mass: 14533.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Plasmid: PET22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: E7FH77*PLUS | ||
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#2: Chemical | ChemComp-ACT / | ||
#3: Chemical | #4: 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: 2.9 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | Temperature: 293 K / pH: 4.5 Details: 32% MPEG 2K, 0.2M ammonium sulfate, 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 27, 2009 / Details: MIRRORS |
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: 1.8→50 Å / Num. obs: 16327 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.095 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LJD Resolution: 1.8→24.81 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.8→24.81 Å
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