+Open data
-Basic information
Entry | Database: PDB / ID: 3tch | ||||||
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Title | Crystal structure of E. coli OppA in an open conformation | ||||||
Components | Periplasmic oligopeptide-binding protein | ||||||
Keywords | PROTEIN TRANSPORT / peptide-binding domain / peptide transport / ABC transporter | ||||||
Function / homology | Function and homology information oligopeptide import across plasma membrane / oligopeptide binding / oligopeptide transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chaperone-mediated protein folding / protein transport / outer membrane-bounded periplasmic space / response to heat / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å | ||||||
Authors | Klepsch, M.M. / Kovermann, M. / Low, C. / Balbach, J. / de Gier, J.W. / Slotboom, D.J. / Berntsson, R.P.-A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Escherichia coli peptide binding protein OppA has a preference for positively charged peptides. Authors: Klepsch, M.M. / Kovermann, M. / Low, C. / Balbach, J. / Permentier, H.P. / Fusetti, F. / de Gier, J.W. / Slotboom, D.J. / Berntsson, R.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tch.cif.gz | 234.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tch.ent.gz | 195.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/3tch ftp://data.pdbj.org/pub/pdb/validation_reports/tc/3tch | 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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-Components
#1: Protein | Mass: 59387.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1243, JW1235, oppA / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P23843 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 8000, glycerol, pH 6.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Feb 26, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→50 Å / Num. obs: 41615 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.535 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.38 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→37.39 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2185 / WRfactor Rwork: 0.1786 / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8796 / SU B: 7.818 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1695 / SU Rfree: 0.1515 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.41 Å2 / Biso mean: 31.6446 Å2 / Biso min: 12.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→37.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.032 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 15.9843 Å / Origin y: 18.4006 Å / Origin z: 28.4687 Å
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