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- PDB-7wda: Crystal structure LpqY in complex with Trehalose from Mycobacteri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wda | ||||||
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Title | Crystal structure LpqY in complex with Trehalose from Mycobacterium tuberculosis | ||||||
![]() | Trehalose-binding lipoprotein LpqY | ||||||
![]() | SUGAR BINDING PROTEIN / Mycobacterium tuberculosis / LpqY / Trehalose / SugABC | ||||||
Function / homology | ![]() trehalose transmembrane transporter activity / trehalose transport / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex / periplasmic space / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, D. / Das, U. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of LpqY, a substrate-binding protein from the SugABC transporter of Mycobacterium tuberculosis, provides insights into its trehalose specificity. Authors: Sharma, D. / Singh, M. / Kaur, P. / Das, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 739 KB | Display | ![]() |
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PDB format | ![]() | 544.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 65.8 KB | Display | |
Data in CIF | ![]() | 96.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wcjSC S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47353.098 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lpqY, Rv1235 / Plasmid: pET / Production host: ![]() ![]() #2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.83 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG |
-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: Nov 26, 2021 / Details: Vertical CRL / Horizontal Eliptical mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→48.03 Å / Num. obs: 137970 / % possible obs: 99.52 % / Redundancy: 12.9 % / Biso Wilson estimate: 33.12 Å2 / CC1/2: 0.998 / CC star: 0.99 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.07 / Net I/σ(I): 8.43 |
Reflection shell | Resolution: 1.91→1.97 Å / Redundancy: 11.6 % / Rmerge(I) obs: 4.29 / Mean I/σ(I) obs: 0.54 / Num. unique obs: 13670 / CC1/2: 0.279 / Rpim(I) all: 1.3 / % possible all: 95.83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7WCJ Resolution: 1.91→48.03 Å / SU ML: 0.2805 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.1014 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→48.03 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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