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- PDB-3mha: Crystal structure of LprG from Mycobacterium tuberculosis bound to PIM -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mha | ||||||
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Title | Crystal structure of LprG from Mycobacterium tuberculosis bound to PIM | ||||||
![]() | Lipoprotein lprG | ||||||
![]() | LIPID BINDING PROTEIN / Lipoprotein / LprG / glycolipid binding protein / Structural Genomics / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | ![]() bacterial extracellular vesicle / glycolipid binding / lipid transport / Prevention of phagosomal-lysosomal fusion / phosphatidylinositol binding / peptidoglycan-based cell wall / response to antibiotic / lipid binding / cell surface / extracellular region ...bacterial extracellular vesicle / glycolipid binding / lipid transport / Prevention of phagosomal-lysosomal fusion / phosphatidylinositol binding / peptidoglycan-based cell wall / response to antibiotic / lipid binding / cell surface / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsai, H.-C. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: Mycobacterium tuberculosis lipoprotein LprG (Rv1411c) binds triacylated glycolipid agonists of Toll-like receptor 2. Authors: Drage, M.G. / Tsai, H.C. / Pecora, N.D. / Cheng, T.Y. / Arida, A.R. / Shukla, S. / Rojas, R.E. / Seshadri, C. / Moody, D.B. / Boom, W.H. / Sacchettini, J.C. / Harding, C.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.2 KB | Display | ![]() |
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PDB format | ![]() | 68 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769.3 KB | Display | ![]() |
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Full document | ![]() | 780.6 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mh8SC ![]() 3mh9C S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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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Unit cell |
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Components
#1: Protein | Mass: 21464.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-Z69 / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100mM Sodium acetate trihydrate, 25% PEG3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2009 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→50 Å / Num. all: 41304 / Num. obs: 35778 / % possible obs: 86.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.052 / Rsym value: 0.061 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2021 / Rsym value: 0.721 / % possible all: 82.2 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6_289) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 3MH8 Resolution: 1.85→32.047 Å / SU ML: 0.25 / σ(F): 1.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.697 Å2 / ksol: 0.332 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→32.047 Å
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Refine LS restraints |
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LS refinement shell |
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