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Yorodumi- PDB-4ruw: The crystal structure of endonuclease/exonuclease/phosphatase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ruw | ||||||
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Title | The crystal structure of endonuclease/exonuclease/phosphatase from Beutenbergia cavernae DSM 12333 | ||||||
Components | Endonuclease/exonuclease/phosphatase | ||||||
Keywords | HYDROLASE / METALLOENZYME / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha/beta/alpha fold / ion / cytosolic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Beutenbergia cavernae DSM 12333 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.281 Å | ||||||
Authors | Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of endonuclease/exonuclease/phosphatase from Beutenbergia cavernae DSM 12333 Authors: Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ruw.cif.gz | 166.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ruw.ent.gz | 136.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ruw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/4ruw ftp://data.pdbj.org/pub/pdb/validation_reports/ru/4ruw | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 46390.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Beutenbergia cavernae DSM 12333 (bacteria) Strain: DSM 12333 / Gene: Bcav_3678 / Plasmid: MCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC References: UniProt: C5C3L1, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #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: 2.49 Å3/Da / Density % sol: 50.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M Sodium Acetate:HCl pH 4.6 8% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2012 / Details: MIRRORS |
Radiation | Monochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→50 Å / Num. all: 114702 / Num. obs: 114702 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 14.28 Å2 / Rsym value: 0.085 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.0819 / Num. unique all: 5822 / Rsym value: 0.239 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.281→26.393 Å / SU ML: 0.08 / σ(F): 1.39 / Phase error: 10.71 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.281→26.393 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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