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Yorodumi- PDB-6nwm: Structures of the transcriptional regulator BgaR, a lactose sensor. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nwm | |||||||||
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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: 2.11 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 | 6nwm.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nwm.ent.gz | 63 KB | Display | PDB format |
PDBx/mmJSON format | 6nwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/6nwm ftp://data.pdbj.org/pub/pdb/validation_reports/nw/6nwm | HTTPS FTP |
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-Related structure data
Related structure data | 6nwhSC 6nwjC 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: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 1 - 162 / Label seq-ID: 1 - 162
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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: 56.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5 mg/mL protein; 1.27 M sodium malonate, 100 mM HEPES pH 7.5. Sitting drops were set up in 200 nL plus 200 nL volumes with seeds 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: 0.953723 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953723 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→46.4 Å / Num. obs: 36663 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.048 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.776 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2389 / CC1/2: 0.761 / Rpim(I) all: 0.498 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6nwh Resolution: 2.11→43.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.811 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.132 / 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: 34.343 Å2
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Refinement step | Cycle: 1 / Resolution: 2.11→43.8 Å
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Refine LS restraints |
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