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- PDB-5kst: Stationary phase Survival protein E (SurE) from Xylella fastidios... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kst | ||||||
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Title | Stationary phase Survival protein E (SurE) from Xylella fastidiosa- XfSurE-TSAmp (Tetramer Smaller - crystallization with 3'AMP). | ||||||
![]() | 5'-nucleotidase SurE | ||||||
![]() | HYDROLASE / Stationary phase survival protein E (SurE) / Xylella fastidiosa / crystallization. | ||||||
Function / homology | ![]() 3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / nucleotide binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Machado, A.T.P. / Fonseca, E.M.B. / Dos Reis, M.A. / Saraiva, A.M. / Dos Santos, C.A. / De Toledo, M.A.S. / Polikarpov, I. / De Souza, A.P. / Aparicio, R. / Iulek, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational variability of the stationary phase survival protein E from Xylella fastidiosa revealed by X-ray crystallography, small-angle X-ray scattering studies, and normal mode analysis. Authors: Machado, A.T.P. / Fonseca, E.M.B. / Reis, M.A.D. / Saraiva, A.M. / Santos, C.A.D. / de Toledo, M.A.S. / Polikarpov, I. / de Souza, A.P. / Aparicio, R. / Iulek, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 404.7 KB | Display | ![]() |
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PDB format | ![]() | 333.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.7 KB | Display | ![]() |
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Full document | ![]() | 493.5 KB | Display | |
Data in XML | ![]() | 40.5 KB | Display | |
Data in CIF | ![]() | 54.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ksqC ![]() 5ksrC ![]() 5kssC ![]() 3ty2S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 29490.037 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 9a5c / Gene: surE, XF_0858 / Production host: ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-IOD / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.1 M bis-tris propane pH 7.6, 0.14 M Sodium iodide, 20% (W/V) PEG 3350, 5 mM dithiotheitol and 0.1 manganese II chloride. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.428 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→77.957 Å / Num. obs: 24993 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.47 % / Rsym value: 0.096 / Net I/σ(I): 16.58 |
Reflection shell | Resolution: 2.76→2.84 Å / Redundancy: 5.13 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 3.4 / % possible all: 92.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TY2 Resolution: 2.759→77.957 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.759→77.957 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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