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- PDB-4r2k: Crystal structure of H119A mutant of YdaA (Universal Stress Prote... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r2k | ||||||
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Title | Crystal structure of H119A mutant of YdaA (Universal Stress Protein E) from Salmonella typhimurium | ||||||
![]() | Universal stress protein E | ||||||
![]() | METAL BINDING PROTEIN / UNKNOWN FUNCTION / ![]() ![]() ![]() ![]() | ||||||
Function / homology | Rossmann fold - #12370 / UspA / Universal stress protein family / ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bangera, M. / Murthy, M.R.N. | ||||||
![]() | ![]() Title: Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance. Authors: Bangera, M. / Panigrahi, R. / Sagurthi, S.R. / Savithri, H.S. / Murthy, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.8 KB | Display | ![]() |
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PDB format | ![]() | 115.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4r2jSC ![]() 4r2lC ![]() 4r2mC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37221.477 Da / Num. of mol.: 1 / Mutation: H119A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: LT2 / Gene: STM1661, uspE, ydaA uspE STM1661 / Plasmid: pRSET C / Production host: ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-EDO / ![]() #4: Chemical | ChemComp-OXD / | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.13 % |
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Crystal grow![]() | Temperature: 298 K / Method: under oil, microbatch Details: 2M Ammonium sulfate, Under oil, Microbatch, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2012 / Details: bent collimating mirror and toroid |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.97→39.91 Å / Num. obs: 36482 / % possible obs: 100 % / Redundancy: 14.6 % / Rsym value: 0.086 |
Reflection shell | Resolution: 1.97→2.07 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 7.3 / Rsym value: 0.348 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ID 4R2J Resolution: 1.97→39.46 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.692 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.132 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→39.46 Å
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Refine LS restraints |
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