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Yorodumi- PDB-1bsr: BOVINE SEMINAL RIBONUCLEASE STRUCTURE AT 1.9 ANGSTROMS RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bsr | ||||||
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Title | BOVINE SEMINAL RIBONUCLEASE STRUCTURE AT 1.9 ANGSTROMS RESOLUTION | ||||||
Components | BOVINE SEMINAL RIBONUCLEASE | ||||||
Keywords | HYDROLASE(PHOSPHORIC DIESTER / RNA) | ||||||
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 / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Mazzarella, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Bovine seminal ribonuclease: structure at 1.9 A resolution. Authors: Mazzarella, L. / Capasso, S. / Demasi, D. / Di Lorenzo, G. / Mattia, C.A. / Zagari, A. #1: Journal: Gazz.Chim.Ital. / Year: 1987 Title: Composite Active Sites in Bovine Seminal Ribonuclease Authors: Mazzarella, L. / Mattia, C.A. / Capasso, S. / Di Lorenzo, G. #2: Journal: Biopolymers / Year: 1983 Title: Refinement of the Structure of Bovine Seminal Ribonuclease Authors: Capasso, S. / Giordano, F. / Mattia, C.A. / Mazzarella, L. / Zagari, A. #3: Journal: Gazz.Chim.Ital. / Year: 1979 Title: Low-Resolution Structure of Bovine Seminal Ribonuclease: A Covalent Dimeric Protein Authors: Capasso, S. / Giordano, F. / Mattia, C.A. / Mazzarella, L. / Zagari, A. | ||||||
History |
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Remark 700 | SHEET THE TWO BETA SHEETS OF EACH CHAIN OF THIS STRUCTURE ARE VERY CLOSE TO THOSE OF RNASE A (5RSA, ...SHEET THE TWO BETA SHEETS OF EACH CHAIN OF THIS STRUCTURE ARE VERY CLOSE TO THOSE OF RNASE A (5RSA, REMARK 5), AND A SIMILAR NOTATION HAS BEEN USED, MODIFIED ONLY TO TAKE INTO ACCOUNT THE PRESENCE OF TWO CHAINS. THEREFORE, DUE TO A BULGE OF RESIDUES 88 - 89, THE FIRST SHEET OF CHAIN A (B), COMPOSED OF 3 STRANDS, CONSISTS OF TWO PARTS DENOTED *S1A* AND *S2A* (*S1B* AND *S2B*), HAVING STRAND 1 AND 3 IDENTICAL. FOR CHAIN A (B), ALSO THE SECOND SHEET, FORMED BY 4 STRANDS, IS COMPOSED BY TWO PARTS DENOTED *S3A* AND *S4A* (*S3B* AND *S4B*), HAVING STRANDS 1, 2 AND 3 IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bsr.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bsr.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 1bsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bsr_validation.pdf.gz | 382.2 KB | Display | wwPDB validaton report |
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Full document | 1bsr_full_validation.pdf.gz | 383.5 KB | Display | |
Data in XML | 1bsr_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 1bsr_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/1bsr ftp://data.pdbj.org/pub/pdb/validation_reports/bs/1bsr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 93 / 2: CIS PROLINE - PRO A 114 / 3: CIS PROLINE - PRO B 93 / 4: CIS PROLINE - PRO B 114 | ||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13632.640 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00669 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | FEATURES OF THE STRUCTURE: RESIDUES 1 - 15 OF ONE CHAIN FOLD AGAINST RESIDUES 23 - 124 OF THE OTHER ...FEATURES OF THE STRUCTURE: RESIDUES 1 - 15 OF ONE CHAIN FOLD AGAINST RESIDUES 23 - 124 OF THE OTHER CHAIN. THEREFORE, IN THE DIMER, THE TWO CHAINS PRESENT THEIR N-TERMINI INTERCHANG | Nonpolymer details | A TOTAL OF 113 WATER MOLECULES, AS WELL AS 7 SULFATE ANIONS, WERE INCLUDED AND REFINED AS PART OF ...A TOTAL OF 113 WATER MOLECULES, AS WELL AS 7 SULFATE ANIONS, WERE INCLUDED AND REFINED AS PART OF THE STRUCTURE. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.72 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.1 / Method: batch method | |||||||||||||||||||||||||
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: 1.9 Å / Lowest resolution: 9999 Å / Num. obs: 17217 / % possible obs: 90 % / Observed criterion σ(I): 3 / Num. measured all: 59869 / Rmerge(I) obs: 0.067 / Biso Wilson estimate: 9.2 Å2 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.177 / Rfactor obs: 0.177 / Highest resolution: 1.9 Å Details: A SECOND POSITION HAS BEEN LOCATED AND REFINED FOR THE SIDE CHAINS OF HIS A 119 AND ARG B 71. IN BOTH CHAINS, GLN 60 HAS A CONFORMATION WHICH FALLS OUTSIDE THE ALLOWED REGIONS OF THE ...Details: A SECOND POSITION HAS BEEN LOCATED AND REFINED FOR THE SIDE CHAINS OF HIS A 119 AND ARG B 71. IN BOTH CHAINS, GLN 60 HAS A CONFORMATION WHICH FALLS OUTSIDE THE ALLOWED REGIONS OF THE RAMACHANDRAN MAP, AS OBSERVED IN RNASE A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 16492 / σ(I): 3 / Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.7 |