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- PDB-2e6b: Crystal structure of the stationary phase survival protein SurE f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2e6b | ||||||
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Title | Crystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8 in complex with magnesium and tungstate | ||||||
![]() | 5'-nucleotidase surE | ||||||
![]() | HYDROLASE / SurE protein / complex with magnesium and tungstate ions | ||||||
Function / homology | ![]() 3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Iwasaki, W. / Miki, K. | ||||||
![]() | ![]() Title: Crystal Structure of the Stationary Phase Survival Protein SurE with Metal Ion and AMP Authors: Iwasaki, W. / Miki, K. | ||||||
History |
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Remark 300 | BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) ...BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) forming a tetramer. This protein is in a dimer-tetramer equilibrium in solution. It is unknown whether this protein is functional as a dimer or a tetramer. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.1 KB | Display | ![]() |
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PDB format | ![]() | 153.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2e69SC ![]() 2e6cC ![]() 2e6eC ![]() 2e6gC ![]() 2e6hC S: Starting model for refinement C: citing same article ( |
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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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3 | ![]()
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Unit cell |
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Details | probably tetramer |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 26625.287 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 107 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/WO4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/WO4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-WO4 / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.1M Tris-HCl pH8.5, 0.75M ammonium sulfate, 10% glycerol, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 46054 / % possible obs: 100 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2E69 Resolution: 2.5→46.46 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2580632.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.2048 Å2 / ksol: 0.372867 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→46.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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