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Open data
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Basic information
Entry | Database: PDB / ID: 5ihf | ||||||
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Title | Salmonella Typhimurium VirG-like (STV) protein | ||||||
![]() | VirG-like protein | ||||||
![]() | UNKNOWN FUNCTION / LTxxQ motif / CpxP_like family | ||||||
Function / homology | LTXXQ motif family protein / LTXXQ motif family protein / periplasmic space / PHOSPHATE ION / VirG-like protein / Probable secreted protein (SPI-6 associated)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pandey, N.K. / Ray, S. / Suar, M. / Bhavesh, N.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Salmonella Typhimurium VirG-like (STV) protein Authors: Pandey, N.K. / Ray, S. / Suar, M. / Bhavesh, N.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.1 KB | Display | ![]() |
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PDB format | ![]() | 108.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5io8S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13200.012 Da / Num. of mol.: 2 / Fragment: UNP residues 24-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SL1344 / Gene: SL1344_RS01575 / Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.8 M Sodium Phosphate Monobasic Monohydrate, Potassium Phosphate Dibasic PH range: 4.8-5.4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.576→63.13 Å / Num. obs: 30511 / % possible obs: 97.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.52 Å2 / Rsym value: 0.069 / Net I/av σ(I): 3.969 / Net I/σ(I): 9.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IO8 Resolution: 1.576→43.38 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.57 Å2 / Biso mean: 44.7161 Å2 / Biso min: 19.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.576→43.38 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: 10
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