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- PDB-7o23: C-terminal head domain of the trimeric autotransporter adhesin Bp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o23 | |||||||||
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Title | C-terminal head domain of the trimeric autotransporter adhesin BpaC from Burkholderia pseudomallei fused to a GCN4 anchor | |||||||||
![]() | Autotransporter adhesin BpaC,Autotransporter adhesin BpaC,General control transcription factor GCN4 | |||||||||
![]() | CELL ADHESION / left-handed parallel beta-roll / extracellular | |||||||||
Function / homology | ![]() cell outer membrane / protein transport / membrane => GO:0016020 / cell adhesion / cell surface Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kiessling, A.R. / Goldman, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The C-terminal head domain of Burkholderia pseudomallei BpaC has a striking hydrophilic core with an extensive solvent network. Authors: Kiessling, A.R. / Harris, S.A. / Weimer, K.M. / Wells, G. / Goldman, 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 | ![]() | 197.9 KB | Display | ![]() |
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PDB format | ![]() | 131.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.7 KB | Display | ![]() |
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Full document | ![]() | 442.9 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s6lS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31293.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: 1026b, ATCC 204508 / S288c Gene: bpaC, BP1026B_I1575, GCN4, AAS101, AAS3, ARG9, YEL009C Plasmid: pET28a Details (production host): KanR, T7 promoter, C-terminal His6 tag Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 53 % / Description: Large hexagonal crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein solution at 130 mg/mL in 20 mM Tris-HCl pH 8, 150 mM NaCl. Hit in JCSG IV, E10: 100 nL protein solution + 100 nL reservoir solution 0.1 M HEPES pH 6.5, 0.8 M (NH4)2SO4 Cryoprotection: ...Details: Protein solution at 130 mg/mL in 20 mM Tris-HCl pH 8, 150 mM NaCl. Hit in JCSG IV, E10: 100 nL protein solution + 100 nL reservoir solution 0.1 M HEPES pH 6.5, 0.8 M (NH4)2SO4 Cryoprotection: add 400 nL of 0.15 M HEPES pH 6.5, 1.2 M (NH4)2SO4, 35% Glycerol Temp details: Controlled |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.79 Å / Num. obs: 65740 / % possible obs: 99.53 % / Observed criterion σ(F): 6 / Redundancy: 8 % / Biso Wilson estimate: 12.07 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Net I/σ(I): 6.87 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 6377 / CC1/2: 0.657 / % possible all: 99.28 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3S6L Resolution: 1.4→44.79 Å / SU ML: 0.1998 / Cross valid method: FREE R-VALUE / σ(F): 1.71 / Phase error: 19.2899 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.4 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→44.79 Å
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Refine LS restraints |
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LS refinement shell |
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