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Open data
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Basic information
Entry | Database: PDB / ID: 6ori | |||||||||
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Title | Enterococcal surface protein, partial N-terminal region | |||||||||
![]() | EF0056 | |||||||||
![]() | UNKNOWN FUNCTION / Immunoglobin / biofilm / Enterococcus | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Spiegelman, L. / Zhang, L. / Tezcan, A. / Ghosh, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Enterococcal surface protein, partial N-terminal region (CASP target) Authors: Spiegelman, L. / Zhang, L. / Tezcan, A. / Ghosh, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.6 KB | Display | ![]() |
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PDB format | ![]() | 76.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.6 KB | Display | ![]() |
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Full document | ![]() | 427.3 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: Protein | Mass: 46379.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q9Z4N7 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 37.26 % / Description: large, triangular crystals |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystallization condition: protein: 7.5 mg/mL in 10 mM Tris and 10 mM NaCl Mother liquid: 0.2 M ammonium acetate, pH 7.0, 16% PEG3350, 1 uL mother liquid + 1 uL protein The crystal was ...Details: Crystallization condition: protein: 7.5 mg/mL in 10 mM Tris and 10 mM NaCl Mother liquid: 0.2 M ammonium acetate, pH 7.0, 16% PEG3350, 1 uL mother liquid + 1 uL protein The crystal was soaked in 8.625%(w/v) sodium acrylate, 2.5%(w/v) acrylamide and 0.2%(w/v) bis-acrylamide in mother liquid (0.2 M ammonium acetate, pH 7.0, 16% PEG 3350). after soaking for over 48 hours, the crystal was transferred to 1% APS and 1% TEMED in mother liquid (0.2 M ammonium acetate, pH 7.0, 16% PEG 3350). after 10 min, calcium chloride was added to the crystal with a final concentration of 100 mM. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→47.27 Å / Num. obs: 58580 / % possible obs: 85.4095 % / Redundancy: 3.17 % / Biso Wilson estimate: 8.90025571117 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 410 / % possible all: 78.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Crystals with selenomethionine previously determined by our lab but unpublished Resolution: 1.4→47.27 Å / SU ML: 0.122 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 16.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→47.27 Å
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Refine LS restraints |
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LS refinement shell |
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