[English] 日本語
Yorodumi- PDB-4ryt: Crystal Structure of F222 form of E112A Mutant of Stationary Phas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ryt | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium | ||||||
Components | 5'/3'-nucleotidase SurE | ||||||
Keywords | HYDROLASE / Stationary phase survival protein / Domain swapping / Rossmann fold like / Phosphatase | ||||||
Function / homology | Function and homology information 3'-nucleotidase / exopolyphosphatase / 3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Mathiharan, Y.K. / Murthy, M.R.N. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015 Title: Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein. Authors: Mathiharan, Y.K. / Savithri, H.S. / Murthy, M.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ryt.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ryt.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ryt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ryt_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ryt_full_validation.pdf.gz | 456.8 KB | Display | |
Data in XML | 4ryt_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 4ryt_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/4ryt ftp://data.pdbj.org/pub/pdb/validation_reports/ry/4ryt | HTTPS FTP |
-Related structure data
Related structure data | 4ryuC 4xepC 4xerC 4xgbC 4xgpC 4xh8C 4xj7C 2v4nS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 28557.074 Da / Num. of mol.: 1 / Mutation: E112A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: surE / Plasmid: pRSETC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLysS References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.82 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 7.5 Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M HEPES (pH 7.5), 30% 2-Methyl 2,4-pentanediol, Under Oil, Microbatch method, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 27, 2013 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→46.33 Å / Num. obs: 18453 / % possible obs: 94 % / Redundancy: 4.9 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.112 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.07→2.18 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 2258 / Rsym value: 0.197 / % possible all: 79.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2V4N Resolution: 2.09→36 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.391 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.188 / 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: 31.672 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→36 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.09→2.14 Å / Total num. of bins used: 20
|