+Open data
-Basic information
Entry | Database: PDB / ID: 3rsd | ||||||
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Title | STRUCTURE OF THE D121N 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: 1.6 Å | ||||||
Authors | Schultz, L.W. / Quirk, D.J. / Raines, R.T. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes. Authors: Schultz, L.W. / Quirk, D.J. / 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 | 3rsd.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rsd.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rsd_validation.pdf.gz | 363.8 KB | Display | wwPDB validaton report |
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Full document | 3rsd_full_validation.pdf.gz | 364.4 KB | Display | |
Data in XML | 3rsd_validation.xml.gz | 4 KB | Display | |
Data in CIF | 3rsd_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/3rsd ftp://data.pdbj.org/pub/pdb/validation_reports/rs/3rsd | HTTPS FTP |
-Related structure data
Related structure data | 4rsdC 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
#1: Protein | Mass: 13707.342 Da / Num. of mol.: 1 / Mutation: D121N 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: 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: 2.19 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||
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Crystal grow | Method: batch method / pH: 5.2 Details: LYOPHILIZED D121N RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ ML. CRYSTALLIZATION WAS PERFORMED IN SMALL SILICONIZED TUBES USING THE BATCH METHOD. A SOLUTION (25UL) ...Details: LYOPHILIZED D121N RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ ML. CRYSTALLIZATION WAS PERFORMED IN SMALL SILICONIZED TUBES USING THE BATCH METHOD. A SOLUTION (25UL) OF THE ENZYME WAS MIXED WITH AN EQUAL VOLUME OF 95% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.10 M MES BUFFER, PH 5.2. CRYSTALS APPEARED WITHIN SEVERAL MONTHS., batch method | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: batch method | ||||||||||||||||||||
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: Aug 28, 1995 / 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: 1.6→30 Å / Num. obs: 15756 / % possible obs: 88 % / Observed criterion σ(I): 0.33 / Redundancy: 1.8 % / Rsym value: 0.019 / Net I/σ(I): 31 |
Reflection shell | Resolution: 1.6→1.7 Å / Rsym value: 0.057 / % possible all: 75 |
Reflection | *PLUS % possible obs: 89 % / Num. measured all: 28480 / Rmerge(I) obs: 0.019 |
Reflection shell | *PLUS Rmerge(I) obs: 0.055 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RPH Resolution: 1.6→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: 257 Å2 / ksol: 0.75 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→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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