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Yorodumi- PDB-1rca: STRUCTURE OF THE CRYSTALLINE COMPLEX OF DEOXYCYTIDYLYL-3',5'-GUAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rca | ||||||
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Title | STRUCTURE OF THE CRYSTALLINE COMPLEX OF DEOXYCYTIDYLYL-3',5'-GUANOSINE (3',5'-DCPDG) CO-CRYSTALISED WITH RIBONUCLEASE AT 1.9 ANGSTROMS RESOLUTION. RETROBINDING IN PANCREATIC RNASEA IS INDEPENDENT OF MODE OF INHIBITOR INTROMISSION | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE (ENDORIBONUCLEASE) | ||||||
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: 1.9 Å | ||||||
Authors | Lisgarten, J.N. / Palmer, R.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Structure of the crystalline complex of deoxycytidylyl-3',5'-guanosine (3',5'-dCpdG) cocrystallized with ribonuclease at 1.9 A resolution. Authors: Listgarten, J.N. / Maes, D. / Wyns, L. / Aguilar, C.F. / Palmer, R.A. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Newly Observed Binding Mode in Pancreatic Ribonuclease Authors: Aguilar, C.F. / Thomas, P.J. / Mills, A. / Moss, D.S. / Palmer, R.A. #2: Journal: J.Crystallogr.Spectrosc.Res. / Year: 1984 Title: The Refined Structure of Ribonuclease-A at 1.45 Angstroms Resolution Authors: Borkakoti, N. / Moss, D.S. / Stanford, M.J. / Palmer, R.A. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1982 Title: Ribonuclease-A: Least-Squares Refinement of the Structure at 1.45 Angstroms Resolution Authors: Borkakoti, N. / Moss, D.S. / Palmer, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rca.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rca.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/1rca ftp://data.pdbj.org/pub/pdb/validation_reports/rc/1rca | 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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Atom site foot note | 1: CIS PROLINE - PRO 93 / 2: CIS PROLINE - PRO 114 |
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CO-CRYSTALLIZED COMPLEX / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.55 % |
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Crystal grow | *PLUS Method: unknown / Details: Carlisle, C. H., (1974) J. Mol. Biol., 85, 1. / PH range low: 5.7 / PH range high: 5.2 |
Components of the solutions | *PLUS Conc.: 30-40 % / Common name: ethanol |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.94 Å / Num. obs: 7807 / % possible obs: 89 % / Num. measured all: 17427 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS Highest resolution: 1.94 Å / Lowest resolution: 2.12 Å / % possible obs: 76 % |
-Processing
Software | Name: RESTRAIN / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.218 / Highest resolution: 1.9 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.058 |