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Yorodumi- PDB-1f0v: Crystal structure of an Rnase A dimer displaying a new type of 3D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f0v | ||||||
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Title | Crystal structure of an Rnase A dimer displaying a new type of 3D domain swapping | ||||||
Components |
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Keywords | hydrolase/DNA / domain swapping / crystal / ribonuclease / bovine pancreas / hydrolase-DNA COMPLEX | ||||||
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 / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Liu, Y.S. / Gotte, G. / Libonati, M. / Eisenberg, D.S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: A domain-swapped RNase A dimer with implications for amyloid formation Authors: Liu, Y.S. / Gotte, G. / Libonati, M. / Eisenberg, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f0v.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f0v.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 1f0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f0v_validation.pdf.gz | 502.5 KB | Display | wwPDB validaton report |
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Full document | 1f0v_full_validation.pdf.gz | 523.4 KB | Display | |
Data in XML | 1f0v_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 1f0v_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/1f0v ftp://data.pdbj.org/pub/pdb/validation_reports/f0/1f0v | HTTPS FTP |
-Related structure data
Related structure data | |
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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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4 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 573.430 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Protein | Mass: 13708.326 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-GOL / #5: 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: 3.23 Å3/Da / Density % sol: 61.96 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Phosphate buffer, 16 % PEG 4000, 2 % Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Details: drop contains protein and reservoir solution in a 1:1 ratio | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.072 |
Detector | Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. all: 76047 / Num. obs: 76047 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Num. unique all: 7548 / % possible all: 95 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 813673 |
Reflection shell | *PLUS % possible obs: 95 % |
-Processing
Software |
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Refinement | Resolution: 1.7→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 75824 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.14 Å2 |