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- PDB-3fl1: X-ray structure of the non covalent swapped form of the A19P/Q28L... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fl1 | |||||||||
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Title | X-ray structure of the non covalent swapped form of the A19P/Q28L/K31C/S32C mutant of bovine pancreatic ribonuclease in complex with 2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE | |||||||||
![]() | Ribonuclease pancreatic | |||||||||
![]() | HYDROLASE / 3D-domain swapping / bovine seminal ribonuclease / non-covalent dimer / antitumor activity / quaternary structure flexibility / protein mutations and evolution / Endonuclease / Glycation / Glycoprotein / Nuclease / Secreted | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Merlino, A. / Russo Krauss, I. / Perillo, M. / Mattia, C.A. / Ercole, C. / Picone, D. / Vergara, A. / Sica, F. | |||||||||
![]() | ![]() Title: Toward an antitumor form of bovine pancreatic ribonuclease: The crystal structure of three noncovalent dimeric mutants Authors: Merlino, A. / Russo Krauss, I. / Perillo, M. / Mattia, C.A. / Ercole, C. / Picone, D. / Vergara, A. / Sica, F. #1: ![]() Title: Structure and stability of the non-covalent swapped dimer of bovine seminal ribonuclease: an enzyme tailored to evade ribonuclease protein inhibitor Authors: Sica, F. / Di Fiore, A. / Merlino, A. / Mazzarella, L. #2: ![]() Title: The buried diversity of bovine seminal ribonuclease: shape and cytotoxicity of the swapped non-covalent form of the enzyme Authors: Merlino, A. / Ercole, C. / Picone, D. / Pizzo, E. / Mazzarella, L. / Sica, F. #3: Journal: Protein Sci. / Year: 1995 Title: Hints on the evolutionary design of a dimeric RNase with special bioactions Authors: Di Donato, A. / Cafaro, V. / Romeo, I. / D'Alessio, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.1 KB | Display | ![]() |
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PDB format | ![]() | 49.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fkzC ![]() 3fl0C ![]() 3fl3C ![]() 1kf3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13823.522 Da / Num. of mol.: 2 / Mutation: A19P, Q28L, K31C, S32C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose | #3: Chemical | ChemComp-CGP / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 26% PEG 4000, 0.2M ammonium sulfate, 0.1M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 21, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 20953 / Num. obs: 20953 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.9→1.96 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KF3 Resolution: 1.9→26.79 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→26.79 Å
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Refine LS restraints |
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