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Yorodumi- PDB-3hcq: Structural analysis of the choline binding protein ChoX in a semi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hcq | ||||||
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Title | Structural analysis of the choline binding protein ChoX in a semi-closed and ligand-free conformation | ||||||
Components | Putative choline ABC transporter, periplasmic solute-binding component | ||||||
Keywords | CHOLINE-BINDING PROTEIN / transport / ABC transporter / binding protein / semi-closed | ||||||
Function / homology | Function and homology information choline transport / choline binding / response to stimulus / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / periplasmic space Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Oswald, C. / Smits, S.H.J. / Hoeing, M. / Bremer, E. / Schmitt, L. | ||||||
Citation | Journal: Biol.Chem. / Year: 2009 Title: Structural analysis of the choline-binding protein ChoX in a semi-closed and ligand-free conformation. Authors: Oswald, C. / Smits, S.H. / Hoing, M. / Bremer, E. / Schmitt, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hcq.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hcq.ent.gz | 89.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/3hcq ftp://data.pdbj.org/pub/pdb/validation_reports/hc/3hcq | HTTPS FTP |
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-Related structure data
Related structure data | 2rinS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32302.014 Da / Num. of mol.: 2 / Mutation: G251D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: choX, R02399, SMc02737 / Plasmid: pETNX / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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: 4.8 Details: ChoX crystals were obtained using the hanging drop method at 293 K, against a reservoir solution of 100 mM Na-acetate pH 4.8-5.0 and 15-25% polyethylene glycol 3350. , VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.978 Å | |||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2007 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.89→20 Å / Num. obs: 16055 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.22 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 11 | |||||||||||||||
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1517 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RIN Resolution: 2.89→19.47 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.813 / SU B: 49.017 / SU ML: 0.471 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 5.617 Å2
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Refinement step | Cycle: LAST / Resolution: 2.89→19.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.89→2.963 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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