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- PDB-4xer: Crystal Structure of C2 form of E112A/H234A Mutant of Stationary ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xer | ||||||
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Title | Crystal Structure of C2 form of E112A/H234A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium | ||||||
![]() | 5'/3'-nucleotidase SurE | ||||||
![]() | HYDROLASE / Stationary phase survival protein / Domain swapping / Rossmann fold like / Phosphatase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mathiharan, Y.K. / Murthy, M.R.N. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.2 KB | Display | ![]() |
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PDB format | ![]() | 180.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 495.2 KB | Display | ![]() |
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Full document | ![]() | 509.6 KB | Display | |
Data in XML | ![]() | 48.7 KB | Display | |
Data in CIF | ![]() | 71.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rytC ![]() 4ryuC ![]() 4xepC ![]() 4xgbC ![]() 4xgpC ![]() 4xh8C ![]() 4xj7C ![]() 2v4nS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28490.008 Da / Num. of mol.: 4 / Mutation: E112A, H234A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase, exopolyphosphatase |
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-Non-polymers , 6 types, 886 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / | ||||||
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#3: Chemical | ChemComp-CA / | ||||||
#4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.6 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 4.6 Details: 0.02M Calcium chloride, 0.1M Sodium acetate (pH 4.6), 30 % 2-Methyl 2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2013 |
Radiation | Monochromator: Si(111) monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→40.32 Å / Num. obs: 104677 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.057 / Net I/σ(I): 142 |
Reflection shell | Resolution: 1.97→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V4N Resolution: 1.97→40.32 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.163 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 40.515 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→40.32 Å
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Refine LS restraints |
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