[English] 日本語
Yorodumi- PDB-4r2j: Crystal structure of YdaA (Universal Stress Protein E) from Salmo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r2j | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of YdaA (Universal Stress Protein E) from Salmonella typhimurium | ||||||
Components | Universal stress protein E | ||||||
Keywords | METAL BINDING PROTEIN / UNKNOWN FUNCTION / Universal stress protein / HUP domain / Internal Symmetry / Stress tolerance / ATP binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4r2j.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4r2j.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 4r2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/4r2j ftp://data.pdbj.org/pub/pdb/validation_reports/r2/4r2j | HTTPS FTP |
---|
-Related structure data
Related structure data | 4r2kC 4r2lC 4r2mC 3olqS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 37288.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria) Strain: LT2 / Gene: STM1661, uspE, ydaA uspE STM1661 / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8ZP84 |
---|---|
#5: Sugar |
-Non-polymers , 4 types, 37 molecules
#2: Chemical | ChemComp-ZN / |
---|---|
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.4 % |
---|---|
Crystal grow | Temperature: 298 K / Method: under oil, microbatch / pH: 5.8 Details: 0.2M Magnesium Nitrate hexahydrate, 20% PEG 3350, 10mM Adenosine 5'-(beta,gamma-imido)triphosphate, 0.2% n-dodecyl beta-D-maltoside, pH 5.8, Under oil, Microbatch, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2011 / 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: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→42.88 Å / Num. obs: 13536 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 45.2 Å2 / Rsym value: 0.119 |
Reflection shell | Resolution: 2.36→2.48 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1929 / Rsym value: 0.642 / % possible all: 98.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3OLQ Resolution: 2.36→37.14 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 20.386 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 59.55 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→37.14 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.356→2.417 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 25.405 Å / Origin y: 16.474 Å / Origin z: 6.161 Å
|