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Yorodumi- PDB-1d5d: The role of phenylalanine 8 in the stabilization of the s protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d5d | ||||||
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Title | The role of phenylalanine 8 in the stabilization of the s protein-s peptide interaction: packing and cavities | ||||||
Components |
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Keywords | HYDROLASE / RNASE S MUTANT(F8M) / CAVITY S PROTEIN / S PEPTIDE | ||||||
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: 2.25 Å | ||||||
Authors | Ratnaparkhi, G.S. / Varadarajan, R. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics. Authors: Ratnaparkhi, G.S. / Varadarajan, R. #1: Journal: Proteins: Struct.,Funct.,Genet. / Year: 1999 Title: X-ray crystallographic studies of the denaturation of ribonuclease S Authors: Ratnaparkhi, G.S. / Varadarajan, R. #2: Journal: Biochemistry / Year: 1992 Title: Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities Authors: Varadarajan, R. / Richards, F.M. #3: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d5d.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d5d.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/1d5d ftp://data.pdbj.org/pub/pdb/validation_reports/d5/1d5d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 1717.943 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-15 / Mutation: F8M / Source method: obtained synthetically Details: S15 PEPTIDE SYNTHESIZED BY SOLID PHASE PEPTIDE SYNTHESIS References: UniProt: P61823 |
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#2: Protein | Mass: 11294.749 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-124 / Source method: isolated from a natural source Details: DERIEVED FROM A LIMIT DIGEST OF BOVINE PANCREATIC RNASE A Source: (natural) Bos taurus (cattle) / References: UniProt: P00656, UniProt: P61823*PLUS |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.72 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.75 Details: 3M CSCL, 35% AMMONIUM SULFATE. 0.1 M SODIUM ACETATE, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 20K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: Thomson, J., (1994) Biochemistry, 33, 8587. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 26, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→10 Å / Num. all: 5293 / Num. obs: 4958 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 20.18 |
Reflection shell | Resolution: 2.19→2.4 Å / Redundancy: 11 % / Rmerge(I) obs: 0.42 / % possible all: 100 |
Reflection | *PLUS Num. obs: 4492 |
-Processing
Software |
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Refinement | Resolution: 2.25→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 19.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.37 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 7
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 1 / % reflection Rfree: 10.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.328 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.3 |