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Yorodumi- PDB-5f2z: Crystal structure of membrane associated PatA from Mycobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f2z | ||||||
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Title | Crystal structure of membrane associated PatA from Mycobacterium smegmatis in complex with palmitate - P21 space group | ||||||
Components | Phosphatidylinositol mannoside acyltransferase | ||||||
Keywords | TRANSFERASE / acyltransferase / glycolipid biosynthesis | ||||||
Function / homology | Function and homology information phosphatidylinositol dimannoside acyltransferase / glycolipid biosynthetic process / phosphatidylinositol metabolic process / phospholipid biosynthetic process / acyltransferase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Albesa-Jove, D. / Svetlikova, Z. / Carreras-Gonzalez, A. / Tersa, M. / Sancho-Vaello, E. / Cifuente, J.O. / Mikusova, K. / Guerin, M.E. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Structural basis for selective recognition of acyl chains by the membrane-associated acyltransferase PatA. Authors: Albesa-Jove, D. / Svetlikova, Z. / Tersa, M. / Sancho-Vaello, E. / Carreras-Gonzalez, A. / Bonnet, P. / Arrasate, P. / Eguskiza, A. / Angala, S.K. / Cifuente, J.O. / Kordulakova, J. / ...Authors: Albesa-Jove, D. / Svetlikova, Z. / Tersa, M. / Sancho-Vaello, E. / Carreras-Gonzalez, A. / Bonnet, P. / Arrasate, P. / Eguskiza, A. / Angala, S.K. / Cifuente, J.O. / Kordulakova, J. / Jackson, M. / Mikusova, K. / Guerin, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f2z.cif.gz | 184.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f2z.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 5f2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/5f2z ftp://data.pdbj.org/pub/pdb/validation_reports/f2/5f2z | HTTPS FTP |
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-Related structure data
Related structure data | 5f2tSC 5f31C 5f34C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 34298.754 Da / Num. of mol.: 4 / Fragment: UNP residues 13-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria) Gene: MSMEG_2934, MSMEI_2860 / Plasmid: pJAM2::patA Production host: Mycobacterium smegmatis str. MC2 155 (bacteria) References: UniProt: A0QWG5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-PLM / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM Tris-HCl pH 7.0, 230 mM MgCl2 and 12-16% (w/v) PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2013 |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→92.37 Å / Num. obs: 23420 / % possible obs: 96.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 6.6 |
Reflection shell | Highest resolution: 2.9 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F2T Resolution: 2.9→92.37 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / Phase error: 30.73 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→92.37 Å
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Refine LS restraints |
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LS refinement shell |
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