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Yorodumi- PDB-4r2m: Crystal Structure of R134D mutant of YnaF (Universal Stress Prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r2m | ||||||
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Title | Crystal Structure of R134D mutant of YnaF (Universal Stress Protein F) from Salmonella typhimurium | ||||||
Components | Universal stress protein F | ||||||
Keywords | UNKNOWN FUNCTION / Universal Stress Protein / HUP domain / Stress tolerance / ATP binding / Chloride binding | ||||||
Function / homology | Function and homology information Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bangera, M. / Murthy, M.R.N. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r2m.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r2m.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 4r2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/4r2m ftp://data.pdbj.org/pub/pdb/validation_reports/r2/4r2m | HTTPS FTP |
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-Related structure data
Related structure data | 4r2jC 4r2kC 4r2lSC C: citing same article (ref.) S: Starting model for refinement |
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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: 17300.945 Da / Num. of mol.: 2 / Mutation: R134D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) Strain: LT2 / Gene: STM1652, uspF, ynaF uspF STM1652 / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P67091 #2: Chemical | #3: Chemical | #4: 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: 2.05 Å3/Da / Density % sol: 40.04 % |
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Crystal grow | Temperature: 298 K / Method: under oil, microbatch / pH: 8.5 Details: 30% PEG 4000, 100mM Tris-HCl pH 8.5, 200mM Magnesium chloride, 5mM Adenosine 5'-(beta,gamma-imido)triphosphate, Under oil, Microbatch, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978565 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2014 / 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: 0.978565 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→41.48 Å / Num. obs: 15273 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.12 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2167 / Rsym value: 0.676 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 4R2L Resolution: 2.2→41.48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.425 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.209 / 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: 41.254 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→41.48 Å
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