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Yorodumi- PDB-2rln: THERMODYNAMIC AND STRUCTURAL CONSEQUENCES OF CHANGING A SULPHUR A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rln | ||||||
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Title | THERMODYNAMIC AND STRUCTURAL CONSEQUENCES OF CHANGING A SULPHUR ATOM TO A METHYLENE GROUP IN THE M13NLE MUTATION IN RIBONUCLEASE S | ||||||
Components |
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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 Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.85 Å | ||||||
Authors | Ratnaparkhi, G. / Varadarajan, R. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S. Authors: Thomson, J. / Ratnaparkhi, G.S. / Varadarajan, R. / Sturtevant, J.M. / Richards, F.M. #1: Journal: Biochemistry / Year: 1992 Title: Crystallographic Structures of Ribonuclease S Variants with Nonpolar Substitutions at Position 13: Packing and Cavities Authors: Varadarajan, R. / Richards, F.M. #2: Journal: Biochemistry / Year: 1992 Title: Refinement of the Crystal Structure of Ribonuclease S. Comparison with and between the Various Ribonuclease A Structures Authors: Kim, E.E. / Varadarajan, R. / Wyckoff, H.W. / Richards, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rln.cif.gz | 33.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rln.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 2rln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rln_validation.pdf.gz | 381.7 KB | Display | wwPDB validaton report |
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Full document | 2rln_full_validation.pdf.gz | 382.7 KB | Display | |
Data in XML | 2rln_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 2rln_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/2rln ftp://data.pdbj.org/pub/pdb/validation_reports/rl/2rln | 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: CIS PROLINE - PRO E 93 / 2: CIS PROLINE - PRO E 114 |
-Components
#1: Protein/peptide | Mass: 1732.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P61823*PLUS |
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#2: Protein | Mass: 11973.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Organ: PANCREAS References: UniProt: P00656, UniProt: P61823*PLUS, EC: 3.1.27.5 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Compound details | THIS RNASE S (M13NLE) MUTANT IS ONE OF A SERIES OF MUTANTS OF RNASE S AT POSITION 13. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.04 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.75 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Processing
Software |
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Refinement | Resolution: 1.85→10 Å /
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Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.5 |