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Yorodumi- PDB-1rpf: THE STRUCTURES OF RNASE COMPLEXED WITH 3'-CMP AND D(CPA): ACTIVE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rpf | ||||||
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Title | THE STRUCTURES OF RNASE COMPLEXED WITH 3'-CMP AND D(CPA): ACTIVE SITE CONFORMATION AND CONSERVED WATER MOLECULES | ||||||
Components | RIBONUCLEASE A | ||||||
Keywords | HYDROLASE(PHOSPHORIC DIESTER) | ||||||
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: 2.2 Å | ||||||
Authors | Zegers, I. / Wyns, L. / Palmer, R. | ||||||
Citation | Journal: Protein Sci. / Year: 1994 Title: The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules. Authors: Zegers, I. / Maes, D. / Dao-Thi, M.H. / Poortmans, F. / Palmer, R. / Wyns, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rpf.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rpf.ent.gz | 25.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rpf_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 1rpf_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | 1rpf_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 1rpf_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/1rpf ftp://data.pdbj.org/pub/pdb/validation_reports/rp/1rpf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: ALA 19 - ALA 20 OMEGA = 149.89 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: TYR 92 - PRO 93 OMEGA = 32.48 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: CIS PROLINE - PRO 114 |
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line: S2 / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-C3P / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.11 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. obs: 8395 / % possible obs: 99.7 % / Num. measured all: 43289 / Rmerge(I) obs: 0.103 |
-Processing
Software | Name: RESTRAIN / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→10 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: RESTRAIN / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.155 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |