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- PDB-3fle: SE_1780 protein of unknown function from Staphylococcus epidermidis. -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fle | ||||||
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Title | SE_1780 protein of unknown function from Staphylococcus epidermidis. | ||||||
![]() | SE_1780 protein | ||||||
![]() | structural genomics / unknown function / APC61035.1 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osipiuk, J. / Hatzos, C. / Clancy, S. / Kim, Y. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: X-ray crystal structure of SE_1780 protein of unknown function from Staphylococcus epidermidis. Authors: Osipiuk, J. / Hatzos, C. / Clancy, S. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.3 KB | Display | ![]() |
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PDB format | ![]() | 94.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.3 KB | Display | ![]() |
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Full document | ![]() | 450.5 KB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Details | a putative biological unit is a monomer based on PISA program |
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Components
#1: Protein | Mass: 28644.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.39 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 1000, 0.1 M Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2008 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.488 |
Reflection | Resolution: 2.009→27 Å / Num. obs: 77366 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.114 / Χ2: 2.279 / Net I/σ(I): 15.682 |
Reflection shell | Resolution: 2.02→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2 / Num. unique all: 1793 / Χ2: 0.967 / % possible all: 92.1 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Refinement was performed using twin law -h,-k,l and twin fraction 0.49. Unknown ligands were modeled as waters in chains X and Y. THE FRIEDEL PAIRS WERE USED FOR PHASING.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.195 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.47 Å2 / Biso mean: 33.714 Å2 / Biso min: 11.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.009→26.995 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 98 %
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