+Open data
-Basic information
Entry | Database: PDB / ID: 1tto | ||||||
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Title | Crystal structure of the Rnase T1 variant R2 | ||||||
Components | RNase T1Ribonuclease T1 | ||||||
Keywords | HYDROLASE / ribonuclease / adenine specificity | ||||||
Function / homology | Function and homology information hyphal tip / ribonuclease T1 activity / ribonuclease T1 / cell septum / endonuclease activity / lyase activity / RNA binding Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Hahn, U. / Czaja, R. / Perbandt, M. / Betzel, C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2005 Title: Purine activity of RNase T1RV is further improved by substitution of Trp59 by tyrosine Authors: Czaja, R. / Perbandt, M. / Betzel, C. / Hahn, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tto.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tto.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 1tto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/1tto ftp://data.pdbj.org/pub/pdb/validation_reports/tt/1tto | HTTPS FTP |
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-Related structure data
Related structure data | 1q9eS 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: 11106.709 Da / Num. of mol.: 3 / Mutation: k41e, y42f, n43r, y45w, e46n, w59y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Plasmid: pA2T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00651, EC: 3.1.27.3 #2: Chemical | #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: 2.2 Å3/Da / Density % sol: 43.8 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG4000, tris-Cl, calcium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 |
Detector | Date: Apr 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Biso Wilson estimate: 13.3 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q9E Resolution: 2.1→48.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1817657.65 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.0963 Å2 / ksol: 0.343661 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→48.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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