+Open data
-Basic information
Entry | Database: PDB / ID: 1c9v | ||||||
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Title | H12A VARIANT OF RIBONUCLEASE A | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE / ANTIPARALLEL BETA SHEET | ||||||
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 / Resolution: 1.7 Å | ||||||
Authors | Park, C. / Schultz, L.W. / Raines, R.T. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Contribution of the active site histidine residues of ribonuclease A to nucleic acid binding. Authors: Park, C. / 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 | 1c9v.cif.gz | 34.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c9v.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 1c9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c9v_validation.pdf.gz | 369.2 KB | Display | wwPDB validaton report |
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Full document | 1c9v_full_validation.pdf.gz | 372 KB | Display | |
Data in XML | 1c9v_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 1c9v_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c9v ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c9v | HTTPS FTP |
-Related 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: 13641.257 Da / Num. of mol.: 1 / Mutation: H12A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Organ: PANCREAS / Plasmid: PET22B+ / Production host: Escherichia coli (E. coli) / 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: 2.87 Å3/Da / Density % sol: 57.11 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30% ammonium sulfate, 50% sodium chloride, 100mM sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 275 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Apr 2, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 20142 / % possible obs: 96 % / Observed criterion σ(I): 0.33 / Redundancy: 2.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.13 / % possible all: 88 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 0.33 / Redundancy: 2.5 % / Num. measured all: 50643 / Rmerge(I) obs: 0.03 / Biso Wilson estimate: 0 Å2 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å / % possible obs: 88 % |
-Processing
Software |
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Refinement | Resolution: 1.7→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Bsol: 289.8 Å2 / ksol: 0.943 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 / Classification: refinement | |||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.182 | |||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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