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Yorodumi- PDB-1srn: THE REFINED CRYSTAL STRUCTURE OF A FULLY ACTIVE SEMISYNTHETIC RIB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1srn | ||||||
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Title | THE REFINED CRYSTAL STRUCTURE OF A FULLY ACTIVE SEMISYNTHETIC RIBONUCLEASE AT 1.8 ANGSTROMS RESOLUTION | ||||||
Components | (RIBONUCLEASE A) x 2 | ||||||
Keywords | HYDROLASE (NUCLEIC ACID / 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 Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Martin, P.D. / Doscher, M.S. / Edwards, B.F.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1987 Title: The refined crystal structure of a fully active semisynthetic ribonuclease at 1.8-A resolution. Authors: Martin, P.D. / Doscher, M.S. / Edwards, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1srn.cif.gz | 38.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1srn.ent.gz | 26.9 KB | Display | PDB format |
PDBx/mmJSON format | 1srn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1srn_validation.pdf.gz | 393 KB | Display | wwPDB validaton report |
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Full document | 1srn_full_validation.pdf.gz | 406.2 KB | Display | |
Data in XML | 1srn_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1srn_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/1srn ftp://data.pdbj.org/pub/pdb/validation_reports/sr/1srn | 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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Unit cell |
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Atom site foot note | 1: RESIDUE 93 IS A CIS-PROLINE. |
-Components
#1: Protein | Mass: 13050.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 |
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#2: Protein/peptide | Mass: 1531.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P61823 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Compound details | FEATURES OF THE STRUCTURE 1. IN SPITE OF AN EIGHT-RESIDUE REDUNANCY BETWEEN RNASE 1 - 118 AND RNASE ...FEATURES OF THE STRUCTURE 1. IN SPITE OF AN EIGHT-RESIDUE REDUNANCY BETWEEN RNASE 1 - 118 AND RNASE 111 - 124, NO REDUNDANT STRUCTURE IS SEEN IN THE CRYSTAL. RESIDUES 114 - 118 OF RNASE 1 - 118 AND RESIDUES 111 - 113 OF RNASE 111 - 124 DO NOT APPEAR IN THE MAP. 2. HIS 119 IS PREDOMINAN |
Nonpolymer details | A TOTAL OF 115 WATER MOLECULES WERE INCLUDED IN THE LAST FOUR CYCLES OF REFINEMENT. A SULFATE ANION ...A TOTAL OF 115 WATER MOLECULES WERE INCLUDED IN THE LAST FOUR CYCLES OF REFINEMENT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.27 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Details: THE MOTHER LIQUOR WAS 80 PER CENT SATURATED AMMONIUM SULFATE, PH 5.2. | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.7 / Method: macro seeding / Details: took Sasaki et al., 1979a from original paper | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rmerge(I) obs: 2 |
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Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2.3 Å / % possible obs: 57 % / Num. possible: 8542 / Num. unique obs: 4828 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 1.8→10 Å / Rfactor obs: 0.204 / σ(F): 2 | ||||||||||||
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 / Num. reflection obs: 121117 / σ(I): 2 / Rfactor obs: 0.204 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |