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- PDB-1j9l: CRYSTAL STRUCTURE OF SURE PROTEIN FROM T.MARITIMA IN COMPLEX WITH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j9l | ||||||
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Title | CRYSTAL STRUCTURE OF SURE PROTEIN FROM T.MARITIMA IN COMPLEX WITH VANADATE | ||||||
![]() | STATIONARY PHASE SURVIVAL PROTEIN | ||||||
![]() | UNKNOWN FUNCTION / vanadate complex / SURE PROTEIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
![]() | Suh, S.W. / Lee, J.Y. / Kwak, J.E. / Moon, J. | ||||||
![]() | ![]() Title: Crystal structure and functional analysis of the SurE protein identify a novel phosphatase family. Authors: Lee, J.Y. / Kwak, J.E. / Moon, J. / Eom, S.H. / Liong, E.C. / Pedelacq, J.D. / Berendzen, J. / Suh, S.W. #1: ![]() Title: Crystallization and preliminary X-ray crystallographic analysis of the surE protein from Thermotoga maritima Authors: Kwak, J.E. / Ha, K.S. / Lee, J.Y. / Im, Y.J. / Park, S.H. / Eom, S.H. / Suh, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.1 KB | Display | ![]() |
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PDB format | ![]() | 90.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1j9jC ![]() 1j9kSC 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: 28107.041 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.04 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 296 KDetails: Kwak, J.E., (2001) Acta Crystallogr., Sect.D, 57, 612. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 17.1 Å2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: surE-tungstate complex (1J9K) Resolution: 1.9→17.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 571286.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.04 Å2 / ksol: 0.388 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 34.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→17.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.4 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.269 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.224 |