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Yorodumi- PDB-6nwj: Structures of the transcriptional regulator BgaR, a lactose sensor. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nwj | |||||||||
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Title | Structures of the transcriptional regulator BgaR, a lactose sensor. | |||||||||
Components | Transcriptional regulator BgaR | |||||||||
Keywords | TRANSCRIPTION / lactose transcriptional regulator / lactose sensor / SAD phasing | |||||||||
Function / homology | Function and homology information sequence-specific DNA binding / DNA-binding transcription factor activity Similarity search - Function | |||||||||
Biological species | Clostridium perfringens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | |||||||||
Authors | Peat, T.S. / Newman, J. | |||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Structures of the transcriptional regulator BgaR, a lactose sensor. Authors: Newman, J. / Caron, K. / Nebl, T. / Peat, T.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nwj.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nwj.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 6nwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/6nwj ftp://data.pdbj.org/pub/pdb/validation_reports/nw/6nwj | HTTPS FTP |
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-Related structure data
Related structure data | 6nwhSC 6nwmC 6nwoC 6nx3C S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 1 - 161 / Label seq-ID: 1 - 161
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-Components
#1: Protein | Mass: 21248.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria) Strain: 13 / Type A / Gene: CPE0770 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XMB9 #2: Polysaccharide | #3: Water | ChemComp-HOH / | |
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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: 2.84 Å3/Da / Density % sol: 56.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 5 mg/mL protein; 1.25 M sodium malonate, 100 mM gly-gly pH 8.2 set up in 200 nL plus 200 nL sitting drops at 20C |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953657 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953657 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→46.4 Å / Num. obs: 26514 / % possible obs: 99 % / Redundancy: 13 % / CC1/2: 0.996 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.06 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.16→2.22 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.167 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2098 / CC1/2: 0.827 / Rpim(I) all: 0.335 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6nwh Resolution: 2.16→43.54 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.219 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.161 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.175 Å2
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Refinement step | Cycle: 1 / Resolution: 2.16→43.54 Å
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Refine LS restraints |
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