+Open data
-Basic information
Entry | Database: PDB / ID: 3hgy | ||||||
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Title | Crystal Structure of CmeR Bound to Taurocholic Acid | ||||||
Components | CmeR | ||||||
Keywords | Transcription repressor / drug binding / Alpha-helical / Helix-Turn-Helix / DNA-binding / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.416 Å | ||||||
Authors | Routh, M.D. / Yang, F. | ||||||
Citation | Journal: To be Published Title: Structural basis for anionic ligand recognition by multidrug binding proteins: crystal structures of CmeR-bile acid complexes Authors: Routh, M.D. / Yang, F. / Su, C.-C. / Zhang, Q. / Yu, E.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hgy.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hgy.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/3hgy ftp://data.pdbj.org/pub/pdb/validation_reports/hg/3hgy | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 25091.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Campylobacter jejuni (Campylobacter) / References: UniProt: Q7B8P6 |
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#2: Chemical | ChemComp-TCH / |
#3: 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: 2.08 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 24% PEG 3350, 0.1M Tris 8.5, 0.1M Magnesium Chloride, 5% JM600, 20mM Sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2009 / Details: Mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 8018 / % possible obs: 99 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 4.1 % / Biso Wilson estimate: 48.77 Å2 / Rmerge(I) obs: 0.102 / Χ2: 0.971 / Net I/σ(I): 10.685 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1487 / Χ2: 1.077 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.416→36.358 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.777 / SU ML: 0.42 / σ(F): 0.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.605 Å2 / ksol: 0.314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.73 Å2 / Biso mean: 73.151 Å2 / Biso min: 35.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.416→36.358 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Origin x: 13.1239 Å / Origin y: 18.352 Å / Origin z: 16.2421 Å
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Refinement TLS group |
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