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Yorodumi- PDB-3mpl: Crystal Structure of Bordetella pertussis BvgS VFT2 domain (Doubl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mpl | ||||||
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Title | Crystal Structure of Bordetella pertussis BvgS VFT2 domain (Double Mutant F375E/Q461E) | ||||||
Components | Virulence sensor protein bvgS | ||||||
Keywords | SIGNALING PROTEIN / VENUS FLYTRAP / SENSOR DOMAIN | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bordetella pertussis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Herrou, J. / Bompard, C. / Wintjens, R. / Dupre, E. / Willery, E. / Villeret, V. / Locht, C. / Antoine, R. / Jacob-Dubuisson, F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Periplasmic domain of the sensor-kinase BvgS reveals a new paradigm for the Venus flytrap mechanism. Authors: Herrou, J. / Bompard, C. / Wintjens, R. / Dupre, E. / Willery, E. / Villeret, V. / Locht, C. / Antoine, R. / Jacob-Dubuisson, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mpl.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mpl.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/3mpl ftp://data.pdbj.org/pub/pdb/validation_reports/mp/3mpl | HTTPS FTP |
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-Related structure data
Related structure data | 3mpkSC 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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-Components
#1: Protein | Mass: 29537.352 Da / Num. of mol.: 1 / Fragment: UNP Residues 287-542 / Mutation: F375E/Q461E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: TohamaI / Gene: BP1877, bvgS / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16575 | ||
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#2: Chemical | #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: 2.26 Å3/Da / Density % sol: 45.49 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 0.085M HEPES (pH 7.5), 10% PEG 40000 (w/v), 6.8% ethylene glycol, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 15270 / % possible obs: 94.1 % / Redundancy: 6.97 % / Rsym value: 0.084 / Net I/σ(I): 20.74 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 6.83 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 6.89 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MPK Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.897 / SU B: 4.414 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.193 / 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: 25.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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