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Yorodumi- PDB-2gbz: The Crystal Structure of XC847 from Xanthomonas campestris: a 3-5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gbz | ||||||
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Title | The Crystal Structure of XC847 from Xanthomonas campestris: a 3-5 Oligoribonuclease of DnaQ fold family with a Novel Opposingly-Shifted Helix | ||||||
Components | OligoribonucleaseOligonucleotidase | ||||||
Keywords | HYDROLASE / 3'-5' oligoribonuclease / Orn / DEDDh / Xanthomonas campestris / structural genomics | ||||||
Function / homology | Function and homology information 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / nucleic acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Chin, K.H. / Yang, C.Y. / Chou, C.C. / Wang, A.H.J. / Chou, S.H. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: The crystal structure of XC847 from Xanthomonas campestris: a 3'-5' oligoribonuclease of DnaQ fold family with a novel opposingly shifted helix Authors: Chin, K.H. / Yang, C.Y. / Chou, C.C. / Wang, A.H.J. / Chou, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gbz.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gbz.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 2gbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/2gbz ftp://data.pdbj.org/pub/pdb/validation_reports/gb/2gbz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21805.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Species: Xanthomonas campestris / Strain: pv. campestris / Production host: Escherichia coli (E. coli) References: UniProt: Q8P8S1, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.62 % |
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Crystal grow | Temperature: 295 K / Method: liquid diffusion / pH: 6.8 Details: Tris 0.1M pH 8.5, MgCl2 0.24M, PEG4KMME 25%, pH 6.8, LIQUID DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.8 Å / Num. all: 12608 / Num. obs: 12418 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28 Å2 |
Reflection shell | Highest resolution: 2.1 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→23.88 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 509336.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.608 Å2 / ksol: 0.310183 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→23.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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