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- PDB-7nbz: Crystal structure of ligand free open conformation of sulfoquinov... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nbz | ||||||
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Title | Crystal structure of ligand free open conformation of sulfoquinovosyl binding protein (SQBP) from Agrobacterium tumefaciens | ||||||
![]() | Sulfoquinovosyl binding protein | ||||||
![]() | SUGAR BINDING PROTEIN / apo / binding protein / sulfoquinovose | ||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / ACETATE ION / Maltose-binding periplasmic protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Snow, A. / Sharma, M. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / ...Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / Ascher, D.B. / McConville, M.J. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.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 | ![]() | 445.5 KB | Display | ![]() |
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PDB format | ![]() | 368.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.3 KB | Display | ![]() |
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Full document | ![]() | 457.1 KB | Display | |
Data in XML | ![]() | 54.4 KB | Display | |
Data in CIF | ![]() | 85 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bbyC ![]() 7bbzC ![]() 7bc0C ![]() 7bc1C ![]() 7ofxC ![]() 7ofyC ![]() 7oh2C ![]() 7olfC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44074.840 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2275825 Å3/Da / Density % sol: 44.81749 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.3 M Ammonium Acetate 0.1 M Bis-TRIS pH 5.5 25% w/v PEG 3350 |
-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: Dec 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→72.014 Å / Num. obs: 234884 / % possible obs: 93.3 % / Redundancy: 2.1 % / CC1/2: 0.995 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.35→1.37 Å / Num. unique obs: 8434 / CC1/2: 0.906 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: D_1292108223 Resolution: 1.35→72.014 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.186 / Average fsc free: 0.9747 / Average fsc work: 0.9812 / Cross valid method: FREE R-VALUE / ESU R: 0.013 / ESU R Free: 0.014 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.291 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→72.014 Å
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Refine LS restraints |
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LS refinement shell |
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