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Yorodumi- PDB-8alo: Heterodimer formation of sensory domains of Vibrio cholerae regul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8alo | ||||||
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Title | Heterodimer formation of sensory domains of Vibrio cholerae regulators ToxR and ToxS | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Vibrio cholerae / transcription regulator / protein complex / ToxR / ToxS / hetero complex | ||||||
Function / homology | Function and homology information phosphorelay response regulator activity / regulation of DNA-templated transcription / DNA binding / plasma membrane Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å | ||||||
Authors | Gubensaek, N. / Sagmeister, T. / Pavkov-Keller, T. / Zangger, K. / Buhlheller, C. / Wagner, G.E. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Elife / Year: 2023 Title: Vibrio cholerae's ToxRS bile sensing system. Authors: Gubensak, N. / Sagmeister, T. / Buhlheller, C. / Geronimo, B.D. / Wagner, G.E. / Petrowitsch, L. / Grawert, M.A. / Rotzinger, M. / Berger, T.M.I. / Schafer, J. / Uson, I. / Reidl, J. / ...Authors: Gubensak, N. / Sagmeister, T. / Buhlheller, C. / Geronimo, B.D. / Wagner, G.E. / Petrowitsch, L. / Grawert, M.A. / Rotzinger, M. / Berger, T.M.I. / Schafer, J. / Uson, I. / Reidl, J. / Sanchez-Murcia, P.A. / Zangger, K. / Pavkov-Keller, T. #1: Journal: Mol Microbiol / Year: 2021 Title: The periplasmic domains of Vibrio cholerae ToxR and ToxS are forming a strong heterodimeric complex independent on the redox state of ToxR cysteines. Authors: Gubensaek, N. / Wagner, G.E. / Schrank, E. / Falsone, F.S. / Berger, T.M.I. / Pavkov-Keller, T. / Reidl, J. / Zangger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8alo.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8alo.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 8alo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8alo_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
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Full document | 8alo_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 8alo_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 8alo_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/8alo ftp://data.pdbj.org/pub/pdb/validation_reports/al/8alo | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11649.107 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: toxR, VC_0984 / Production host: Escherichia coli (E. coli) / References: UniProt: P15795 |
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#2: Protein | Mass: 18681.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: toxS, VC_0983 / Production host: Escherichia coli (E. coli) / References: UniProt: P24003 |
#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: 1.99 Å3/Da / Density % sol: 38.13 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 30mg/ml of ToxRSp in Tris buffer (20mM Tris, 150mM NaCl, pH7), 0.5 microliters of protein was mixed with 0.5 microliters of crystal condition (0.2 M Magnesium chloride hexahydrate. 0.1 M BIS- ...Details: 30mg/ml of ToxRSp in Tris buffer (20mM Tris, 150mM NaCl, pH7), 0.5 microliters of protein was mixed with 0.5 microliters of crystal condition (0.2 M Magnesium chloride hexahydrate. 0.1 M BIS-Tris. 5.5. 25 % w/v PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9677 Å | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 8, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3→62.793 Å / Num. obs: 4790 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.059 / Rrim(I) all: 0.123 / Net I/σ(I): 12.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Alphafold Model Resolution: 3.002→62.793 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: FREE R-VALUE / ESU R Free: 0.497 Details: Hydrogens have been used if present in the input file
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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 PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.359 Å2
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Refinement step | Cycle: LAST / Resolution: 3.002→62.793 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: 20
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