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Open data
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Basic information
Entry | Database: PDB / ID: 4o8s | ||||||
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Title | Crystal structure of JHP933 from Helicobacter pylori | ||||||
![]() | Putative | ||||||
![]() | HYDROLASE / nucleotidyl transferase | ||||||
Function / homology | ![]() JHP933, helical tail domain / JHP933, nucleotidyltransferase-like core domain / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nuclear Transport Factor 2; Chain: A, / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, Y.H. / Su, Y.T. / Sun, L.F. / Wu, Y. | ||||||
![]() | ![]() Title: Crystal Structure Confirmation of JHP933 as a Nucleotidyltransferase Superfamily Protein from Helicobacter pylori Strain J99 Authors: Zhao, Y. / Ye, X. / Su, Y. / Sun, L. / She, F. / Wu, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.2 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412 KB | Display | ![]() |
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Full document | ![]() | 414 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.5 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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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
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Components
#1: Protein | Mass: 26935.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.06 % / Mosaicity: 0.23 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Potassium Sodium tartarate, 0.1M Tris-HCl, 32%(v/w) PEG4000, pH 7.5, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→50 Å / Num. obs: 20549 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.139 / Χ2: 1.821 / Net I/σ(I): 9.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.442 Å2 / ksol: 0.346 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.43 Å2 / Biso mean: 47.0548 Å2 / Biso min: 21.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→38.005 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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