+Open data
-Basic information
Entry | Database: PDB / ID: 3rsk | ||||||
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Title | STRUCTURE OF THE K7A/R10A/K66A VARIANT OF RIBONUCLEASE A | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE / ENDONUCLEASE / RIBONUCLEASE A / SITE-DIRECTED MUTAGENESIS | ||||||
Function / homology | Function and homology information pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Schultz, L.W. / Fisher, B.M. / Raines, R.T. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Coulombic Effects of Remote Subsites on the Active Site of Ribonuclease A Authors: Fisher, B.M. / Schultz, L.W. / Raines, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rsk.cif.gz | 34.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rsk.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rsk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rsk_validation.pdf.gz | 375.8 KB | Display | wwPDB validaton report |
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Full document | 3rsk_full_validation.pdf.gz | 376.4 KB | Display | |
Data in XML | 3rsk_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 3rsk_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/3rsk ftp://data.pdbj.org/pub/pdb/validation_reports/rs/3rsk | HTTPS FTP |
-Related structure data
Related structure data | 4rskC 1rphS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13506.006 Da / Num. of mol.: 1 / Mutation: K7A, R10A, K66A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line: BL21 / Organ: PANCREAS / Plasmid: PBXR / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61823, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-ACT / |
#3: 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: 3.25 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.5 Details: CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD. LYOPHILIZED K7A/R10A/K66A RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ML. DROPS CONSISTING OF PROTEIN SOLUTION ...Details: CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD. LYOPHILIZED K7A/R10A/K66A RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ML. DROPS CONSISTING OF PROTEIN SOLUTION (1.5UL), WATER (1.5UL), AND RESERVOIR SOLUTION (3.0UL) WERE SUSPENDED OVER 0.5 ML OF RESERVOIR SOLUTION [0.1M SODIUM ACETATE BUFFER, PH 4.5, CONTAINING 36% PEG 4000., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Sep 11, 1997 / Details: LONG MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 33804 / % possible obs: 91 % / Observed criterion σ(I): 0.33 / Redundancy: 2.3 % / Rsym value: 0.023 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2→2.1 Å / Rsym value: 0.17 / % possible all: 84 |
Reflection | *PLUS Num. obs: 14929 / Num. measured all: 33804 / Rmerge(I) obs: 0.029 |
Reflection shell | *PLUS % possible obs: 84 % / Rmerge(I) obs: 0.171 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RPH Resolution: 2→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 156 Å2 / ksol: 0.61 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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