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- PDB-4xh8: Crystal Structure of E112A/D230A Mutant of Stationary Phase Survi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xh8 | ||||||
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Title | Crystal Structure of E112A/D230A 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 | ![]() | 102.5 KB | Display | ![]() |
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PDB format | ![]() | 75.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.9 KB | Display | ![]() |
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Full document | ![]() | 451.4 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rytC ![]() 4ryuC ![]() 4xepC ![]() 4xerC ![]() 4xgbC ![]() 4xgpC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28513.066 Da / Num. of mol.: 2 / Mutation: E112A, D230A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase, exopolyphosphatase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.08M Magnesium chloride, 0.1M HEPES (pH 7.5), 15 % polyacrylic acid sodium salt |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2013 / 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: 3.56→49.3 Å / Num. obs: 6585 / % possible obs: 81.2 % / Redundancy: 4.3 % / Rsym value: 0.193 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 3.56→3.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.8 / % possible all: 82.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V4N Resolution: 3.56→44.14 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.852 / SU B: 39.317 / SU ML: 0.597 / Cross valid method: THROUGHOUT / ESU R Free: 0.889 / 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: 73.592 Å2
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Refinement step | Cycle: 1 / Resolution: 3.56→44.14 Å
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Refine LS restraints |
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