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Yorodumi- PDB-4gho: Crystal Structure Analysis of Streptomyces aureofaciens Ribonucle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gho | ||||||
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Title | Crystal Structure Analysis of Streptomyces aureofaciens Ribonuclease S24A mutant | ||||||
Components | Guanyl-specific ribonuclease Sa | ||||||
Keywords | HYDROLASE / Structural Genomics / Enzyme Function Initiative / Alpha helix / three-stranded beta sheet | ||||||
Function / homology | Function and homology information ribonuclease T1 activity / ribonuclease T1 / RNA endonuclease activity / lyase activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces aureofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Sevcik, J. / Urbanikova, L. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Contribution of hydrogen bonds to protein stability Authors: Pace, C.N. / Fu, H. / Fryar, K.L. / Landua, J. / Trevino, S.R. / Schell, D. / Thurlkill, R.L. / Imura, S. / Scholtz, J.M. / Gajiwala, K. / Sevcik, J. / Urbanikova, L. / Myers, J.K. / Takano, ...Authors: Pace, C.N. / Fu, H. / Fryar, K.L. / Landua, J. / Trevino, S.R. / Schell, D. / Thurlkill, R.L. / Imura, S. / Scholtz, J.M. / Gajiwala, K. / Sevcik, J. / Urbanikova, L. / Myers, J.K. / Takano, K. / Hebert, E.J. / Shirley, B.A. / Grimsley, G.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gho.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gho.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 4gho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/4gho ftp://data.pdbj.org/pub/pdb/validation_reports/gh/4gho | HTTPS FTP |
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-Related structure data
Related structure data | 4j5gC 4j5kC 1rggS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10566.492 Da / Num. of mol.: 2 / Mutation: S24A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Gene: rnaSA, U39467 / Production host: Escherichia coli (E. coli) / References: UniProt: P05798, EC: 3.1.27.3 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.7M ammonium sulfate, phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.834 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 13, 1998 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.834 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→20 Å / Num. all: 99693 / Num. obs: 80959 / % possible obs: 98.2 % |
Reflection shell | Resolution: 1.1→1.11 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 2619 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RGG Resolution: 1.1→14.52 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.576 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→14.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.128 Å / Total num. of bins used: 20
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