[English] 日本語
Yorodumi- PDB-4ryu: Crystal Structure of C2 form of E112A Mutant of Stationary Phase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ryu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of C2 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 / 3'-nucleotidase activity / exopolyphosphatase / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Enteritidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 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 | 4ryu.cif.gz | 228 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ryu.ent.gz | 182.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ryu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/4ryu ftp://data.pdbj.org/pub/pdb/validation_reports/ry/4ryu | HTTPS FTP |
---|
-Related structure data
Related structure data | 4rytC 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 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28557.074 Da / Num. of mol.: 4 / Mutation: E112A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Enteritidis (bacteria) Strain: EC20130345 / Gene: AV66_15865, surE / Plasmid: pRSETC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLysS References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase |
---|
-Non-polymers , 5 types, 954 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MPD / ( #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.57 % |
---|---|
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: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 11, 2012 / 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: 2.03→47.87 Å / Num. obs: 89024 / % possible obs: 98.6 % / Redundancy: 4 % / Biso Wilson estimate: 29.96 Å2 / Rsym value: 0.085 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 11902 / Rsym value: 0.534 / % possible all: 91 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2V4N Resolution: 2.04→48 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.738 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.143 / 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: 32.645 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→48 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.04→2.09 Å / Total num. of bins used: 20
|