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- PDB-3wai: Crystal structure of the C-terminal globular domain of oligosacch... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wai | ||||||
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Title | Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (AfAglB-L, O29867_ARCFU) from Archaeoglobus fulgidus as a MBP fusion | ||||||
![]() | Maltose-binding periplasmic protein, Transmembrane oligosaccharyl transferase | ||||||
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Function / homology | ![]() dolichyl-phosphooligosaccharide-protein glycotransferase / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matsumoto, S. / Shimada, A. / Kohda, D. | ||||||
![]() | ![]() Title: Crystal structure of the C-terminal globular domain of the third paralog of the Archaeoglobus fulgidus oligosaccharyltransferases Authors: Matsumoto, S. / Shimada, A. / Kohda, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 303.5 KB | Display | ![]() |
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PDB format | ![]() | 244.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pebS 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
#1: Protein | Mass: 82973.312 Da / Num. of mol.: 1 Fragment: UNP residues of MBP 27-392, C-terminal globular domain residues 500-868 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() Strain: K12, DSM 4304 / Gene: malE, aglB-L / Plasmid: pET47b(+) / Production host: ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4 Details: 0.1M CAPSO, 33% PEG 3350, pH 9.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 26, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.897→50 Å / Num. all: 58464 / Num. obs: 58383 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2926 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1PEB Resolution: 1.897→29.793 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8762 / SU ML: 0.2 / σ(F): 0 / Phase error: 19.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.2 Å2 / Biso mean: 27.8309 Å2 / Biso min: 8.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.897→29.793 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: 21
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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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