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Yorodumi- PDB-3ub6: Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ub6 | ||||||
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Title | Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with urea 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 / SIRAS / Resolution: 1.38 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 | 3ub6.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ub6.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ub6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/3ub6 ftp://data.pdbj.org/pub/pdb/validation_reports/ub/3ub6 | 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 590 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-GOL / #6: 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: 3.72 Å3/Da / Density % sol: 66.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M PIPES pH 6.5, 22% PEG 3350, 0.2 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: 5.0.3 / Wavelength: 0.977 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2008 / Details: Rh/Pt coated | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.38→50 Å / Num. all: 127039 / Num. obs: 126318 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.071 / Χ2: 0.932 / Net I/σ(I): 13.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.38→47.27 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1385 / WRfactor Rwork: 0.1153 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9437 / SU B: 0.841 / SU ML: 0.016 / SU R Cruickshank DPI: 0.0335 / SU Rfree: 0.0344 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.034 / 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: 65.54 Å2 / Biso mean: 18.2775 Å2 / Biso min: 6.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→47.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.381→1.417 Å / Total num. of bins used: 20
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