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Yorodumi- PDB-5f31: Crystal structure of membrane associated PatA from Mycobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f31 | ||||||
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Title | Crystal structure of membrane associated PatA from Mycobacterium smegmatis in complex with palmitate - P 42 21 2 space group | ||||||
Components | Phosphatidylinositol mannoside acyltransferase | ||||||
Keywords | TRANSFERASE / acyltransferase / glycolipid biosynthesis | ||||||
Function / homology | Function and homology information phosphatidylinositol dimannoside acyltransferase / glycolipid biosynthetic process / phospholipid biosynthetic process / phosphatidylinositol metabolic process / acyltransferase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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 | 5f31.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f31.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 5f31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f31_validation.pdf.gz | 585.3 KB | Display | wwPDB validaton report |
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Full document | 5f31_full_validation.pdf.gz | 585.4 KB | Display | |
Data in XML | 5f31_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 5f31_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f31 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f31 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34298.754 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-PLM / |
#3: Chemical | ChemComp-EOH / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl pH 8.5 and 20% ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99996 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→40.19 Å / Num. obs: 14652 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 4.6 |
Reflection shell | Highest resolution: 2.43 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→40.187 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.71 / 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: 2.43→40.187 Å
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Refine LS restraints |
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LS refinement shell |
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