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- PDB-4xep: Crystal Structure of F222 form of E112A/H234A Mutant of Stationar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xep | ||||||
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Title | Crystal Structure of F222 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 | ![]() | 133 KB | Display | ![]() |
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PDB format | ![]() | 102 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.6 KB | Display | ![]() |
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Full document | ![]() | 462.5 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rytC ![]() 4ryuC ![]() 4xerC ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28490.008 Da / Num. of mol.: 1 / 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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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-PO4 / | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 0.02 M MgCl2 hexahydrate, 22% (w/v) Polyacrylic acid 5100 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: 1.5→50 Å / Num. obs: 49090 / % possible obs: 95.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 68.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.4 / % possible all: 75.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2V4N Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.08 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.082 / 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: 32.593 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→50 Å
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Refine LS restraints |
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