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Yorodumi- PDB-3bry: Crystal structure of the Ralstonia pickettii toluene transporter TbuX -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bry | ||||||
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Title | Crystal structure of the Ralstonia pickettii toluene transporter TbuX | ||||||
Components | TbuX | ||||||
Keywords | TRANSPORT PROTEIN / beta barrel / outer membrane protein | ||||||
Function / homology | : / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Porin / Beta Barrel / Mainly Beta / TbuX Function and homology information | ||||||
Biological species | Ralstonia pickettii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Hearn, E.M. / Patel, D.R. / van den Berg, B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation. Authors: Hearn, E.M. / Patel, D.R. / van den Berg, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bry.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bry.ent.gz | 122.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bry_validation.pdf.gz | 657.5 KB | Display | wwPDB validaton report |
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Full document | 3bry_full_validation.pdf.gz | 706 KB | Display | |
Data in XML | 3bry_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 3bry_validation.cif.gz | 46.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/3bry ftp://data.pdbj.org/pub/pdb/validation_reports/br/3bry | HTTPS FTP |
-Related structure data
-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: 46276.641 Da / Num. of mol.: 2 / Fragment: sequence database residues 26-458 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: PKO1 / Gene: tbuX / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q9RBW8 #2: Chemical | |
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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: 2.86 Å3/Da / Density % sol: 56.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG 4000, 0.1 M magnesium acetate, 50 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9198 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2006 |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→31.92 Å / Num. all: 27405 / Num. obs: 27405 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 2.74→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The starting model was a partial structure of TbuX that was determined from a SAD dataset but did not refine well.
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Displacement parameters | Biso mean: 47.29 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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