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Yorodumi- PDB-7rsa: STRUCTURE OF PHOSPHATE-FREE RIBONUCLEASE A REFINED AT 1.26 ANGSTROMS -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rsa | |||||||||
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Title | STRUCTURE OF PHOSPHATE-FREE RIBONUCLEASE A REFINED AT 1.26 ANGSTROMS | |||||||||
Components | RIBONUCLEASE APancreatic ribonuclease family | |||||||||
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: 1.26 Å | |||||||||
Authors | Wlodawer, A. / Gilliland, G.L. | |||||||||
Citation | Journal: Biochemistry / Year: 1988 Title: Structure of phosphate-free ribonuclease A refined at 1.26 A. Authors: Wlodawer, A. / Svensson, L.A. / Sjolin, L. / Gilliland, G.L. #1: 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. #2: 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. #3: 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 | 7rsa.cif.gz | 58.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rsa.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 7rsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/7rsa ftp://data.pdbj.org/pub/pdb/validation_reports/rs/7rsa | 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: RESIDUES 93 AND 114 ARE CIS PROLINES. / 2: SEE REMARK 4. |
-Components
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell line: S2 / Organ: PANCREAS References: UniProt: P00656, UniProt: P61823*PLUS, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-TBU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.25 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.3 / Method: unknown / Details: used microseeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.26 Å / Num. all: 30947 / Num. obs: 25732 / Num. measured all: 129694 / Rmerge(I) obs: 0.05 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.15 / Highest resolution: 1.26 Å Details: SOME WATER MOLECULES ARE CLOSER THAN 2.8 ANGSTROMS FROM OTHER WATER MOLECULES. THEY MAY REPRESENT ALTERNATELY OCCUPIED SITES OR SEPARATE NETWORKS. SEE THE PAPER CITED ON THE *JRNL* RECORDS ...Details: SOME WATER MOLECULES ARE CLOSER THAN 2.8 ANGSTROMS FROM OTHER WATER MOLECULES. THEY MAY REPRESENT ALTERNATELY OCCUPIED SITES OR SEPARATE NETWORKS. SEE THE PAPER CITED ON THE *JRNL* RECORDS ABOVE FOR MORE DETAILS. SOME ATOMS IN RESIDUES 7 AND 31 HAVE AN OCCUPANCY LESS THAN 1.0. THESE ATOMS WERE POORLY DEFINED IN THE ELECTRON DENSITY AND THEIR OCCUPANCY WAS LOWERED. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.26 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 23398 / σ(F): 2 / Rfactor obs: 0.15 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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