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Yorodumi- PDB-1rcn: CRYSTAL STRUCTURE OF THE RIBONUCLEASE A D(APTPAPAPG) COMPLEX : DI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rcn | ||||||
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Title | CRYSTAL STRUCTURE OF THE RIBONUCLEASE A D(APTPAPAPG) COMPLEX : DIRECT EVIDENCE FOR EXTENDED SUBSTRATE RECOGNITION | ||||||
Components |
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Keywords | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / 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 / Resolution: 2.32 Å | ||||||
Authors | Fontecilla-Camps, J.C. / De Llorens, R. / Le Du, M.H. / Cuchillo, C.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1994 Title: Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition. Authors: Fontecilla-Camps, J.C. / de Llorens, R. / le Du, M.H. / Cuchillo, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rcn.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rcn.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 1rcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/1rcn ftp://data.pdbj.org/pub/pdb/validation_reports/rc/1rcn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1198.856 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / Secretion: MILK / References: UniProt: P61823, EC: 3.1.27.5 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.91 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.3 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 5664 / Redundancy: 3.9 % / Rmerge(I) obs: 0.129 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.32→8 Å / σ(F): 2 Details: OLIGONUCLEOTIDE STEREOCHEMISTRY: NUCLEOTIDE SUGAR PUCKER BASE A1 C2'-ENDO SYN T2 C2'-ENDO ANTI A3 C3'-ENDO ANTI A4 C3'-ENDO ANTI
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Refinement step | Cycle: LAST / Resolution: 2.32→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.32 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.57 |