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- PDB-5oce: THE MOLECULAR MECHANISM OF SUBSTRATE RECOGNITION AND CATALYSIS OF... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oce | ||||||
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Title | THE MOLECULAR MECHANISM OF SUBSTRATE RECOGNITION AND CATALYSIS OF THE MEMBRANE ACYLTRANSFERASE PatA -- Complex of PatA with palmitate, mannose, and palmitoyl-6-mannose | ||||||
![]() | Phosphatidylinositol mannoside acyltransferase | ||||||
![]() | TRANSFERASE / acyltransferase / glycolipid biosynthesis | ||||||
Function / homology | ![]() phosphatidylinositol dimannoside acyltransferase / glycolipid biosynthetic process / phospholipid biosynthetic process / phosphatidylinositol metabolic process / acyltransferase activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Albesa-Jove, D. / Tersa, M. / Guerin, M.E. | ||||||
![]() | ![]() Title: The Molecular Mechanism of Substrate Recognition and Catalysis of the Membrane Acyltransferase PatA from Mycobacteria. Authors: Tersa, M. / Raich, L. / Albesa-Jove, D. / Trastoy, B. / Prandi, J. / Gilleron, M. / Rovira, C. / Guerin, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 355.7 KB | Display | ![]() |
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PDB format | ![]() | 294.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5f2tS S: Starting model for refinement |
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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: 33591.062 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MSMEG_2934, MSMEI_2860 / Production host: ![]() References: UniProt: A0QWG5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-PLM / | #3: Sugar | ChemComp-BMA / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: The crystal of PatA was obtained by mixing 0.25ul of the protein (5 mg ml-1) in 5 mM D-(+)-mannose and 20 mM Tris-HCl buffer pH 7.5 with 0.25ul of a mother liquor containing, 100 mM Tris-HCl ...Details: The crystal of PatA was obtained by mixing 0.25ul of the protein (5 mg ml-1) in 5 mM D-(+)-mannose and 20 mM Tris-HCl buffer pH 7.5 with 0.25ul of a mother liquor containing, 100 mM Tris-HCl pH 7.0, 225 mM MgCl2 and 16% (w/v) PEG 8,000. PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→28.77 Å / Num. obs: 40218 / % possible obs: 97.17 % / Redundancy: 3.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1125 / Net I/σ(I): 12.76 |
Reflection shell | Resolution: 2.41→2.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4939 / Num. unique obs: 3754 / CC1/2: 0.773 / % possible all: 90.55 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5F2T Resolution: 2.41→28.77 Å / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 22.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→28.77 Å
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Refine LS restraints |
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LS refinement shell |
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