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Yorodumi- PDB-3ub9: Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ub9 | ||||||
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Title | Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with hydroxyurea bound | ||||||
Components | chemoreceptor TlpB | ||||||
Keywords | MEMBRANE PROTEIN / homodimer / four-helix bundle / PAS domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Henderson, J.N. / Sweeney, E.G. / Goers, J. / Wreden, C. / Hicks, K.G. / Parthasarathy, R. / Guillemin, K.J. / Remington, S.J. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Structure and proposed mechanism for the pH-sensing Helicobacter pylori chemoreceptor TlpB. Authors: Goers Sweeney, E. / Henderson, J.N. / Goers, J. / Wreden, C. / Hicks, K.G. / Foster, J.K. / Parthasarathy, R. / Remington, S.J. / Guillemin, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ub9.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ub9.ent.gz | 133 KB | Display | PDB format |
PDBx/mmJSON format | 3ub9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/3ub9 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/3ub9 | 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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 20687.516 Da / Num. of mol.: 2 / Fragment: Periplasmic portion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: SS1 / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6JPK4*PLUS #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 7.0, 2.0 M ammonium sulfate, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2008 / Details: Rh/Pt coated Si | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.42→50 Å / Num. all: 116572 / Num. obs: 113775 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Χ2: 0.916 / Net I/σ(I): 13.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→40.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1539 / WRfactor Rwork: 0.1289 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9376 / SU B: 1.039 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0388 / SU Rfree: 0.0393 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.11 Å2 / Biso mean: 17.1805 Å2 / Biso min: 5.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→40.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.421→1.458 Å / Total num. of bins used: 20
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