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Yorodumi- PDB-5d6u: X-ray crystal structure of ribonuclease A determined for the real... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d6u | ||||||
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Title | X-ray crystal structure of ribonuclease A determined for the real space D/H contrast method | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / Ribonuclease A / D/H contrast | ||||||
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 / Resolution: 1.52 Å | ||||||
Authors | Chatake, T. / Fujiwara, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography Authors: Chatake, T. / Fujiwara, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d6u.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d6u.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 5d6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d6u ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6u | 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 | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Pancreas / References: UniProt: P61823, EC: 3.1.27.5 |
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#2: Chemical | ChemComp-IPA / |
#3: 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: 43.41 % / Description: H2O-solvent crystal of ribonuclease A |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 5.8 Details: 20 mg/mL ribonuclease A, 0.05 M sodium acetate, 50% 2-propanol |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→16.9 Å / Num. obs: 16748 / % possible obs: 91.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 43.3 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 20.8 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Resolution: 1.52→16.861 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 11.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.799 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.52→16.861 Å
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Refine LS restraints |
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LS refinement shell |
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