+Open data
-Basic information
Entry | Database: PDB / ID: 3rsp | ||||||
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Title | STRUCTURE OF THE P93G VARIANT OF RIBONUCLEASE A | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | ENDONUCLEASE / HYDROLASE / 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: 1.7 Å | ||||||
Authors | Schultz, L.W. / Hargraves, S.R. / Klink, T.A. / Raines, R.T. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Structure and stability of the P93G variant of ribonuclease A. Authors: Schultz, L.W. / Hargraves, S.R. / Klink, T.A. / 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 | 3rsp.cif.gz | 37 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rsp.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rsp_validation.pdf.gz | 416.9 KB | Display | wwPDB validaton report |
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Full document | 3rsp_full_validation.pdf.gz | 417.7 KB | Display | |
Data in XML | 3rsp_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 3rsp_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/3rsp ftp://data.pdbj.org/pub/pdb/validation_reports/rs/3rsp | HTTPS FTP |
-Related structure data
Related structure data | 1rphS 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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Unit cell |
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-Components
#1: Protein | Mass: 13668.264 Da / Num. of mol.: 1 / Mutation: P93G 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 | #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: 3.02 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: 6UL DROPS COMPOSED OF 15MG/ML PROTEIN,50MM SODIUM ACETATE AT PH 6.0, 15% SATURATED AMMONIUM SULFATE AND 25% SATURATED SODIUM CHLORIDE WERE SUSPENDED OVER 0.5ML WELLS CONTAINING 100MM SODIUM ...Details: 6UL DROPS COMPOSED OF 15MG/ML PROTEIN,50MM SODIUM ACETATE AT PH 6.0, 15% SATURATED AMMONIUM SULFATE AND 25% SATURATED SODIUM CHLORIDE WERE SUSPENDED OVER 0.5ML WELLS CONTAINING 100MM SODIUM ACETATE, PH 6.0, 30% SATURATED AMMONIUM SULFATE AND 50% SATURATED SODIUM CHLORIDE. TEMPERATURE: 20C., 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: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 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: 1.7→30 Å / Num. obs: 22780 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.028 / Rsym value: 0.028 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 3 / Rsym value: 0.15 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RPH Resolution: 1.7→30 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: THE FOLLOWING RESIDUES WERE MODELED WITH TWO CONFORMATIONS: THR 17, ASN 24, SER 59, ASP 83. ASP 83 MAKES A WATER MEDIATED HYDROGEN BOND VIA HOH 183 WITH OG1 OF THR 45 AND MAKES A DIRECT ...Details: THE FOLLOWING RESIDUES WERE MODELED WITH TWO CONFORMATIONS: THR 17, ASN 24, SER 59, ASP 83. ASP 83 MAKES A WATER MEDIATED HYDROGEN BOND VIA HOH 183 WITH OG1 OF THR 45 AND MAKES A DIRECT HYDROGEN BOND TO OG1 OF THR 45 IN THE B POSITION.
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 221 Å2 / ksol: 0.82 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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