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Yorodumi- PDB-9rsa: CRYSTAL STRUCTURE OF TWO COVALENT NUCLEOSIDE DERIVATIVES OF RIBON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9rsa | ||||||
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Title | CRYSTAL STRUCTURE OF TWO COVALENT NUCLEOSIDE DERIVATIVES OF RIBONUCLEASE A | ||||||
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: 1.8 Å | ||||||
Authors | Nachman, J. / Wlodawer, A. | ||||||
Citation | Journal: Biochemistry / Year: 1990 Title: Crystal structure of two covalent nucleoside derivatives of ribonuclease A. Authors: Nachman, J. / Miller, M. / Gilliland, G.L. / Carty, R. / Pincus, M. / Wlodawer, A. #1: Journal: Biochemistry / Year: 1988 Title: Structure of Phosphate-Free Ribonuclease A Refined at 1.26 Angstroms Authors: Wlodawer, A. / Svensson, L.A. / Sjolin, L. / Gilliland, G.L. #2: Journal: Proteins / Year: 1986 Title: Multiple Conformations of Amino Acid Residues in Ribonuclease A Authors: Svensson, L.A. / Sjolin, L. / Gilliland, G.L. / Finzel, B.C. / Wlodawer, A. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1986 Title: Comparison of Two Independently Refined Models of Ribonuclease-A Authors: Wlodawer, A. / Borkakoti, N. / Moss, D.S. / Howlin, B. #4: Journal: J.Biol.Chem. / Year: 1982 Title: The Refined Crystal Structure of Ribonuclease A at 2.0 Angstroms Resolution Authors: Wlodawer, A. / Bott, R. / Sjolin, L. | ||||||
History |
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Remark 700 | SHEET THIS STRUCTURE CONTAINS TWO SHEETS. SHEET S1 COMPRISES THREE STRANDS. IN THE SECOND STRAND OF ...SHEET THIS STRUCTURE CONTAINS TWO SHEETS. SHEET S1 COMPRISES THREE STRANDS. IN THE SECOND STRAND OF SHEET S1, RESIDUES 88 AND 89 *BULGE OUT*. IN ORDER TO REPRESENT THIS BREAK IN STRAND 2, TWO SHEETS (S1A AND S1B) ARE DEFINED BELOW. STRANDS 1 AND 3 OF *SHEETS* S1A AND S1B ARE, THEREFORE, IDENTICAL AND STRAND 2 DIFFERS. SHEET S2 COMPRISES FOUR STRANDS. RESIDUE 120 DOES NOT PROPERLY BELONG IN STRAND 4 OF SHEET S2. IN ORDER TO REPRESENT THIS BREAK IN STRAND 4, TWO SHEETS (S2A AND S2B) ARE DEFINED BELOW. STRANDS 1,2,3 OF *SHEETS* S2A AND S2B ARE, THEREFORE, IDENTICAL AND STRAND 4 DIFFERS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9rsa.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9rsa.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 9rsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9rsa_validation.pdf.gz | 452.1 KB | Display | wwPDB validaton report |
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Full document | 9rsa_full_validation.pdf.gz | 458.4 KB | Display | |
Data in XML | 9rsa_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 9rsa_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/9rsa ftp://data.pdbj.org/pub/pdb/validation_reports/rs/9rsa | 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: RESIDUES 93 AND 114 OF EACH CHAIN ARE CIS PROLINES. / 2: IN ADU A 125 ONLY THE AMINOACYL LINK IS PRESENT. / 3: SEE REMARK 9. |
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.45 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.1 / Method: unknown / Details: pH was adjusted to 5.1 with acetate buffer | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2 Å / Num. obs: 19632 / Observed criterion σ(I): 1.5 / Num. measured all: 162247 / Rmerge(I) obs: 0.078 |
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-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→10 Å / Rfactor obs: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor obs: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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