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- PDB-5f7v: ABC substrate-binding protein Lmo0181 from Listeria monocytogenes... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f7v | |||||||||
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Title | ABC substrate-binding protein Lmo0181 from Listeria monocytogenes in complex with cycloalternan | |||||||||
![]() | Lmo0181 protein | |||||||||
![]() | CYCLOALTERNAN BINDING PROTEIN / substrate-binding protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Lmo0181 protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Light, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
![]() | ![]() Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis. Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.2 KB | Display | ![]() |
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PDB format | ![]() | 143.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817.2 KB | Display | ![]() |
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Full document | ![]() | 818.8 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kmqC ![]() 5do8C ![]() 5f7pC ![]() 5f7qC ![]() 5f7rC ![]() 5f7sC ![]() 5f7uC 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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Unit cell |
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Components
#1: Protein | Mass: 44792.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-679 / EGD-e / Gene: lmo0181 / Production host: ![]() ![]() |
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#2: Polysaccharide | Cyclic alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.87 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 26 mg/mL protein in 0.05 M sodium chloride, 0.01 M Tris-HCl, pH 8.3, 2 mM cycloalternan against Classics II D4 (Qiagen, 0.1 M citric acid, pH 3.5, 25% w/v PEG3350) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2015 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 64488 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.681 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→29.84 Å
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Refine LS restraints |
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