+Open data
-Basic information
Entry | Database: PDB / ID: 7wcj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure LpqY from Mycobacterium tuberculosis | ||||||
Components | Trehalose-binding lipoprotein LpqY | ||||||
Keywords | SUGAR BINDING PROTEIN / Mycobacterium tuberculosis / LpqY / SugABC | ||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Sharma, D. / Das, U. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7wcj.cif.gz | 517.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7wcj.ent.gz | 398.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/7wcj ftp://data.pdbj.org/pub/pdb/validation_reports/wc/7wcj | HTTPS FTP |
---|
-Related structure data
Related structure data | 7wdaSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 47353.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: lpqY, Rv1235 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WGU9 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å |
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: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→44.38 Å / Num. obs: 45257 / % possible obs: 99.83 % / Redundancy: 20 % / Biso Wilson estimate: 44.03 Å2 / CC1/2: 0.99 / CC star: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.05 / Rrim(I) all: 0.29 / Net I/av σ(I): 9.81 / Net I/σ(I): 14.89 |
Reflection shell | Resolution: 2.24→2.3 Å / Redundancy: 15 % / Rmerge(I) obs: 4.479 / Mean I/σ(I) obs: 1.07 / Num. unique obs: 4453 / CC1/2: 0.531 / Rpim(I) all: 0.91 / % possible all: 99.89 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WDA Resolution: 2.24→44.38 Å / SU ML: 0.2771 / Cross valid method: FREE R-VALUE / Phase error: 31.852 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→44.38 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 31 - 463 / Label seq-ID: 1 - 433
|