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- PDB-2gbz: The Crystal Structure of XC847 from Xanthomonas campestris: a 3-5... -
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Open data
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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 | ||||||
![]() | Oligoribonuclease | ||||||
![]() | HYDROLASE / 3'-5' oligoribonuclease / Orn / DEDDh / Xanthomonas campestris / structural genomics | ||||||
Function / homology | ![]() 3'-5'-RNA exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chin, K.H. / Yang, C.Y. / Chou, C.C. / Wang, A.H.J. / Chou, S.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.4 KB | Display | ![]() |
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PDB format | ![]() | 35.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 364.1 KB | Display | ![]() |
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Full document | ![]() | 365.6 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Species: Xanthomonas campestris / Strain: pv. campestris / Production host: ![]() ![]() 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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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