+Open data
-Basic information
Entry | Database: PDB / ID: 1py3 | ||||||
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Title | Crystal structure of Ribonuclease Sa2 | ||||||
Components | ribonuclease | ||||||
Keywords | HYDROLASE / ALPHA-BETA STRUCTURE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces aureofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sevcik, J. / Dauter, Z. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystal structure reveals two alternative conformations in the active site of ribonuclease Sa2. Authors: Sevcik, J. / Dauter, Z. / Wilson, K.S. #1: Journal: Protein Expr.Purif. / Year: 1997 Title: Purification of Ribonucleases Sa, Sa2 and Sa3 after Expression in Escherichia coli Authors: Hebert, E.J. / Grimsley, G.R. / Hartley, R.W. / Horn, G. / Schell, D. / Garcia, S. / Both, V. / Sevcik, J. / Pace, C.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1py3.cif.gz | 179.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1py3.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 1py3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/1py3 ftp://data.pdbj.org/pub/pdb/validation_reports/py/1py3 | HTTPS FTP |
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-Related structure data
Related structure data | 1pylC 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10909.012 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: R8-26 / Plasmid: pEH100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53752, EC: 3.1.4.8 #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: 3.03 Å3/Da / Density % sol: 59.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: ammonium sulfate, phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9185 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 17, 1996 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9185 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. all: 35955 / Num. obs: 35955 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.96 / Num. unique all: 1759 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RGG Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.443 / SU ML: 0.077 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.109 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.486 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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