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Yorodumi- PDB-1d5e: The role of phenylalanine 8 in the stabilization of the S protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d5e | |||||||||
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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 F8(NORLEUCINE) / 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. / 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 | 1d5e.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d5e.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d5e_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
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Full document | 1d5e_full_validation.pdf.gz | 438.6 KB | Display | |
Data in XML | 1d5e_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 1d5e_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/1d5e ftp://data.pdbj.org/pub/pdb/validation_reports/d5/1d5e | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Monomer. Two fragments S peptide and S protein held together by non-covalent interactions |
-Components
#1: Protein/peptide | Mass: 1699.905 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-15 / Mutation: F8(NLE) / 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 24-124 / 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: 2.17 Å3/Da / Density % sol: 43.23 % | ||||||||||||||||||||||||||||||
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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 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. all: 6089 / Num. obs: 5286 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.45 / Num. unique all: 1109 / % possible all: 95 |
Reflection | *PLUS Num. obs: 4923 |
-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: 17.6 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: 0.037 / 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: 11 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.298 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.289 |