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Yorodumi- PDB-2gej: Crystal Structure of phosphatidylinositol mannosyltransferase (Pi... -
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-Basic information
Entry | Database: PDB / ID: 2gej | ||||||
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Title | Crystal Structure of phosphatidylinositol mannosyltransferase (PimA) from Mycobacterium smegmatis in complex with GDP-Man | ||||||
Components | PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE (PimA) | ||||||
Keywords | TRANSFERASE / GT4 GLYCOSYLTRANSFERASE / MANNOSYLTRANSFERASE / ROSSMANN FOLD / BINARY COMPLEX | ||||||
Function / homology | Function and homology information GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity / phosphatidyl-myo-inositol alpha-mannosyltransferase / phosphatidylinositol alpha-mannosyltransferase activity / glycolipid biosynthetic process / phosphatidylinositol metabolic process / phospholipid biosynthetic process / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Guerin, M.E. / Buschiazzo, A. / Kordulakova, J. / Jackson, M. / Alzari, P.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Molecular recognition and interfacial catalysis by the essential phosphatidylinositol mannosyltransferase PimA from mycobacteria. Authors: Guerin, M.E. / Kordulakova, J. / Schaeffer, F. / Svetlikova, Z. / Buschiazzo, A. / Giganti, D. / Gicquel, B. / Mikusova, K. / Jackson, M. / Alzari, P.M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Crystallization and preliminary crystallographic analysis of PimA, an essential mannosyltransferase from Mycobacterium smegmatis Authors: Guerin, M.E. / Buschiazzo, A. / Kordulakova, J. / Jackson, M. / Alzari, P.M. #2: Journal: J.Biol.Chem. / Year: 2002 Title: Definition of the first mannosylation step in phosphatidylinositol mannoside synthesis Authors: Kordulakova, J. / Gilleron, M. / Mikusova, K. / Puzo, G. / Brennan, P.J. / Gicquel, B. / Jackson, M. #3: Journal: Mol.Microbiol. / Year: 2004 Title: Mycbacterial lipoarabinomannan and related lipoglycans: from biogenesis to modulation of the immune response Authors: Briken, V. / Porcelli, S.A. / Besra, G.S. / Kremer, L. #4: Journal: Biochimie / Year: 2003 Title: Lipoarabinomannans: from structure to biosynthesis Authors: Nigou, J. / Gilleron, M. / Puzo, G. #5: Journal: J.Mol.Biol. / Year: 2003 Title: An evolving hierarchical family classification for glycosyltransferases Authors: Coutinho, P.M. / Deleury, E. / Davies, G.J. / Henrissat, B. | ||||||
History |
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Remark 999 | SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS ENTRY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gej.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gej.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/2gej ftp://data.pdbj.org/pub/pdb/validation_reports/ge/2gej | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43440.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: PIMA / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: A0QWG6 |
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#2: Chemical | ChemComp-GDD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 mM GDP, 10-18% PEG 8000, 200 mM CALCIUM ACETATE, 50 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2004 |
Radiation | Monochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.903 Å / Num. all: 12054 / Num. obs: 12054 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.6→2.74 Å / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.2 / Num. measured all: 6110 / Num. unique obs: 1703 / Rsym value: 0.349 / % possible all: 100 |
-Phasing
Phasing MR | Rfactor: 0.367 / Cor.coef. Fo:Fc: 0.72 / Cor.coef. Io to Ic: 0.697
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 21.978 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.151 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.634 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→49.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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