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- PDB-2gej: Crystal Structure of phosphatidylinositol mannosyltransferase (Pi... -

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Basic information

Entry
Database: PDB / ID: 2gej
TitleCrystal Structure of phosphatidylinositol mannosyltransferase (PimA) from Mycobacterium smegmatis in complex with GDP-Man
ComponentsPHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE (PimA)
KeywordsTRANSFERASE / GT4 GLYCOSYLTRANSFERASE / MANNOSYLTRANSFERASE / ROSSMANN FOLD / BINARY COMPLEX
Function / homology
Function and homology information


GDP-Man:Man(3)GlcNAc(2)-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
: / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / Phosphatidyl-myo-inositol mannosyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGuerin, 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
DepositionMar 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS ENTRY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE (PimA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0462
Polymers43,4401
Non-polymers6051
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.071, 72.747, 137.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE (PimA)


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
#2: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2004
RadiationMonochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Phasing

Phasing MRRfactor: 0.367 / Cor.coef. Fo:Fc: 0.72 / Cor.coef. Io to Ic: 0.697
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.245 894 7.4 %RANDOM
Rwork0.192 ---
all0.196 12013 --
obs0.196 12013 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.634 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å20 Å2
2---2.56 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 39 23 2741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222773
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.9853780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97722.946112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.9715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0851523
X-RAY DIFFRACTIONr_chiral_restr0.1150.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022098
X-RAY DIFFRACTIONr_nbd_refined0.2440.21294
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.26
X-RAY DIFFRACTIONr_mcbond_it0.7421.51835
X-RAY DIFFRACTIONr_mcangle_it1.19222846
X-RAY DIFFRACTIONr_scbond_it2.02531064
X-RAY DIFFRACTIONr_scangle_it3.1664.5934
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 64 -
Rwork0.291 805 -
obs-869 100 %

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