+Open data
-Basic information
Entry | Database: PDB / ID: 2nui | ||||||
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Title | X-ray Structure of synthetic [D83A]RNase A | ||||||
Components | Ribonuclease pancreatic | ||||||
Keywords | HYDROLASE / synthetic protein | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Boerema, D.J. / Tereshko, V.A. / Kent, S.B.H. | ||||||
Citation | Journal: Biopolymers / Year: 2008 Title: Total synthesis by modern chemical ligation methods and high resolution (1.1 A) X-ray structure of ribonuclease A Authors: Boerema, D.J. / Tereshko, V.A. / Kent, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nui.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nui.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 2nui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nui_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 2nui_full_validation.pdf.gz | 445.7 KB | Display | |
Data in XML | 2nui_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 2nui_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/2nui ftp://data.pdbj.org/pub/pdb/validation_reports/nu/2nui | HTTPS FTP |
-Related structure data
Related structure data | 2e3wC 1izpS 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: 13664.316 Da / Num. of mol.: 1 / Mutation: D83A / Source method: obtained synthetically Details: Synthesized using a combination of Boc 'in situ neutralization' solid phase peptide synthesis and native chemical ligation. Source: (synth.) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 | ||||
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#2: Chemical | #3: Chemical | ChemComp-BTB / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.54 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.89 Details: 0.1 M Bis-Tris, 1.0 M ammonium sulfate, 1.5 M NaCl, pH 5.89, Drop 1:1 well:protein solution in H2O, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→20 Å / Num. obs: 59512 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1IZP Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.6 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.452 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
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