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- PDB-4n9w: Crystal structure of phosphatidyl mannosyltransferase PimA -

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Basic information

Entry
Database: PDB / ID: 4n9w
TitleCrystal structure of phosphatidyl mannosyltransferase PimA
ComponentsGDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase
KeywordsTRANSFERASE / GT-B
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
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 / Phosphatidyl-myo-inositol mannosyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsGiganti, D. / Albesa-Jove, D. / Bellinzoni, M. / Guerin, M.E. / Alzari, P.M.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Secondary structure reshuffling modulates glycosyltransferase function at the membrane.
Authors: Giganti, D. / Albesa-Jove, D. / Urresti, S. / Rodrigo-Unzueta, A. / Martinez, M.A. / Comino, N. / Barilone, N. / Bellinzoni, M. / Chenal, A. / Guerin, M.E. / Alzari, P.M.
History
DepositionOct 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0463
Polymers41,5411
Non-polymers5052
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.507, 75.515, 59.326
Angle α, β, γ (deg.)90.00, 97.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase / Alpha-mannosyltransferase / Guanosine diphosphomannose-phosphatidyl-inositol alpha- ...Alpha-mannosyltransferase / Guanosine diphosphomannose-phosphatidyl-inositol alpha-mannosyltransferase / Phosphatidylinositol alpha-mannosyltransferase / PI alpha-mannosyltransferase


Mass: 41541.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_2935, MSMEI_2861, pimA / Plasmid: pET28a-pimA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: A0QWG6, phosphatidylinositol alpha-mannosyltransferase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 8000, 200 mM MgCl2, 100 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0668 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0668 Å / Relative weight: 1
ReflectionResolution: 1.94→22 Å / Num. all: 28505 / Num. obs: 27870 / % possible obs: 98.1 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 3.8 % / Biso Wilson estimate: 24.56 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→21.688 Å / SU ML: 0.24 / σ(F): 0.38 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 1221 5.11 %
Rwork0.1616 --
obs0.1642 23873 98.1 %
all-27870 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→21.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 32 107 2795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112768
X-RAY DIFFRACTIONf_angle_d1.2913782
X-RAY DIFFRACTIONf_dihedral_angle_d13.87990
X-RAY DIFFRACTIONf_chiral_restr0.067440
X-RAY DIFFRACTIONf_plane_restr0.006491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.01760.25051230.19792494X-RAY DIFFRACTION98
2.0176-2.10940.24261260.18372527X-RAY DIFFRACTION98
2.1094-2.22050.23971490.1762502X-RAY DIFFRACTION98
2.2205-2.35950.23331340.16592497X-RAY DIFFRACTION98
2.3595-2.54140.23741340.16652515X-RAY DIFFRACTION98
2.5414-2.79670.21691290.17252521X-RAY DIFFRACTION98
2.7967-3.20020.21211480.17562512X-RAY DIFFRACTION99
3.2002-4.02770.2261460.14852526X-RAY DIFFRACTION98
4.0277-21.68950.16631320.14562558X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.420.34850.58331.8940.16711.56510.09240.14360.109-0.0665-0.06630.1503-0.0936-0.1468-0.03680.18720.0369-0.00920.1612-0.00080.1821-0.0782-2.82993.3732
21.5579-0.8289-0.88445.18962.29043.1742-0.04160.0704-0.0665-0.1172-0.15710.2979-0.0334-0.25870.15530.238-0.0031-0.04950.1675-0.00480.19319.441310.123129.0551
32.5835-0.33521.55171.48880.29682.50180.17840.1443-0.17990.16740.0424-0.1240.42880.1516-0.31910.1763-0.0181-0.01750.11140.01850.196813.4206-9.369313.7901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 176 )
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 329 )
3X-RAY DIFFRACTION3chain 'A' and (resid 330 through 373 )

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