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Yorodumi- PDB-2rej: ABC-transporter choline binding protein in unliganded semi-closed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rej | ||||||
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Title | ABC-transporter choline binding protein in unliganded semi-closed conformation | ||||||
Components | PUTATIVE GLYCINE BETAINE ABC TRANSPORTER PROTEIN | ||||||
Keywords | CHOLINE-BINDING PROTEIN / Type II binding protein / Aromatic box / ABC-transporter / TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information choline transport / choline binding / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / periplasmic space Similarity search - Function | ||||||
Biological species | Rhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Oswald, C. / Smits, S.H.J. / Hoeing, M. / Sohn-Boeser, L. / Le Rudulier, D. / Schmitt, L. / Bremer, E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal structures of the choline/acetylcholine substrate-binding protein ChoX from Sinorhizobium meliloti in the liganded and unliganded-closed states. Authors: Oswald, C. / Smits, S.H. / Hoing, M. / Sohn-Bosser, L. / Dupont, L. / Le Rudulier, D. / Schmitt, L. / Bremer, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rej.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rej.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 2rej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rej_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 2rej_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 2rej_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2rej_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/2rej ftp://data.pdbj.org/pub/pdb/validation_reports/re/2rej | 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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Details | 2 biological units in the asymmetric unit |
-Components
#1: Protein | Mass: 32302.014 Da / Num. of mol.: 2 / Mutation: G251D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium meliloti (bacteria) / Gene: opuC / Production host: Escherichia coli (E. coli) / References: UniProt: Q92N37 |
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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: 2.9 Å3/Da / Density % sol: 57.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M Na acetate pH 5.0, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9 Å |
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Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 22282 / Redundancy: 3.4 % / Rmerge(I) obs: 0.222 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.767 / SU B: 26.351 / SU ML: 0.537 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.85 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Twinning operator is h,-k,-l. Twinning perfect pseudo-merohedral twin.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.398 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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