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- PDB-4nc9: Crystal structure of phosphatidyl mannosyltransferase PimA -

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Basic information

Entry
Database: PDB / ID: 4nc9
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 / phospholipid biosynthetic process / phosphatidylinositol metabolic 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
Phosphatidyl-myo-inositol mannosyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.192 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 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase
B: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase
C: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase
D: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase


Theoretical massNumber of molelcules
Total (without water)166,1654
Polymers166,1654
Non-polymers00
Water1,18966
1
A: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase


Theoretical massNumber of molelcules
Total (without water)41,5411
Polymers41,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase


Theoretical massNumber of molelcules
Total (without water)41,5411
Polymers41,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase


Theoretical massNumber of molelcules
Total (without water)41,5411
Polymers41,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase


Theoretical massNumber of molelcules
Total (without water)41,5411
Polymers41,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase
B: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase


Theoretical massNumber of molelcules
Total (without water)83,0822
Polymers83,0822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-14 kcal/mol
Surface area31530 Å2
MethodPISA
6
C: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase
D: GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase


Theoretical massNumber of molelcules
Total (without water)83,0822
Polymers83,0822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-12 kcal/mol
Surface area31420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.620, 137.620, 168.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )
21chain D and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )
12chain B and (resseq 1:59 or resseq 69:131 or resseq 159:171)
22chain C and (resseq 1:59 or resseq 69:131 or resseq 159:171)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )A-1 - 56
121chain A and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )A69 - 131
131chain A and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )A133 - 272
141chain A and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )A274 - 373
211chain D and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )D-1 - 56
221chain D and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )D69 - 131
231chain D and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )D133 - 272
241chain D and (resseq -1:56 or resseq 69:131 or resseq 133:272 or resseq 274:373 )D274 - 373
112chain B and (resseq 1:59 or resseq 69:131 or resseq 159:171)B1 - 59
122chain B and (resseq 1:59 or resseq 69:131 or resseq 159:171)B69 - 131
132chain B and (resseq 1:59 or resseq 69:131 or resseq 159:171)B159 - 171
212chain C and (resseq 1:59 or resseq 69:131 or resseq 159:171)C1 - 59
222chain C and (resseq 1:59 or resseq 69:131 or resseq 159:171)C69 - 131
232chain C and (resseq 1:59 or resseq 69:131 or resseq 159:171)C159 - 171

NCS ensembles :
ID
1
2

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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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 4000, 200 mM MgCl2, 100 mM Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.0

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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: 3.19→43.52 Å / Num. all: 31022 / Num. obs: 31022 / % possible obs: 99.59 % / Observed criterion σ(F): 1.38 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.061
Reflection shellResolution: 3.19→3.36 Å / Rmerge(I) obs: 0.512 / % possible all: 96.8

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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
Starting model: pdb entry 2GEK

2gek


Resolution: 3.192→43.52 Å / SU ML: 0.41 / σ(F): 1.38 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1567 5.04 %random
Rwork0.2118 ---
obs0.2141 29522 99.58 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.192→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10233 0 0 66 10299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510424
X-RAY DIFFRACTIONf_angle_d0.90314222
X-RAY DIFFRACTIONf_dihedral_angle_d13.1513563
X-RAY DIFFRACTIONf_chiral_restr0.0491682
X-RAY DIFFRACTIONf_plane_restr0.0041868
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4958X-RAY DIFFRACTIONPOSITIONAL0.954
12D4958X-RAY DIFFRACTIONPOSITIONAL0.954
21B1914X-RAY DIFFRACTIONPOSITIONAL0.704
22C1914X-RAY DIFFRACTIONPOSITIONAL0.704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1917-3.29470.34471140.30432597X-RAY DIFFRACTION97
3.2947-3.41240.33031420.25632628X-RAY DIFFRACTION100
3.4124-3.5490.26941300.2342680X-RAY DIFFRACTION100
3.549-3.71040.30051430.25282671X-RAY DIFFRACTION100
3.7104-3.90590.29461400.23362659X-RAY DIFFRACTION100
3.9059-4.15040.23331390.21622657X-RAY DIFFRACTION100
4.1504-4.47060.27421470.19472703X-RAY DIFFRACTION100
4.4706-4.920.22191570.18592685X-RAY DIFFRACTION100
4.92-5.63060.26791720.20612675X-RAY DIFFRACTION100
5.6306-7.0890.27341440.2272732X-RAY DIFFRACTION100
7.089-43.52490.20891390.18542832X-RAY DIFFRACTION99
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)
16.47230.32520.02823.8197-0.55264.5320.27360.85311.4287-0.7228-0.2823-0.8062-0.84391.17710.07290.8255-0.06430.21750.78460.18970.891473.932822.115-19.8132
24.2141-0.09584.30143.7981-1.1596.00660.3920.4626-0.1824-0.0449-0.0969-0.0642-0.0580.2086-0.3380.52460.12120.01780.41970.02480.514959.674211.841-21.8362
32.0174-0.9242-0.79643.81091.3223.433-0.0038-0.75430.69980.5399-0.0309-0.0229-0.22060.33050.08640.6181-0.14130.10260.654-0.16860.736768.47616.89585.3069
46.4725-0.8621-2.57613.84170.6343.21420.2302-1.35271.45311.0347-0.06270.2394-0.81150.2578-0.10671.0377-0.05890.02580.8998-0.43440.971363.720824.285315.3866
59.3368-2.2774-1.33836.9942-0.20694.3198-0.4261-0.5834-0.89511.26670.16080.56130.5693-0.25680.06420.8484-0.06890.13860.5038-0.01810.549562.88618.557310.8357
64.66240.61770.91235.9481-3.14588.12490.35731.3546-0.3454-0.724-0.1064-0.163-0.05710.7841-0.6190.67990.13370.1170.8899-0.02380.717374.88917.3166-21.0281
74.9745-0.3229-0.70554.5815-0.93714.30020.38181.1569-0.9735-0.8892-0.32590.19610.8228-0.01930.02390.93170.2153-0.17650.669-0.26030.657543.83312.5596-37.27
81.5326-0.0790.92799.0511-2.08171.085-0.01720.3640.3442-0.3172-0.1705-0.06590.61560.6314-0.22190.7430.22780.04740.78480.11960.91353.570725.6814-46.0117
91.67191.0876-0.72025.6748-3.39153.6816-0.2261-0.5353-0.86930.6880.17430.44270.6837-0.11240.14171.15690.13280.25380.73830.2181.114830.367-4.2467-8.1433
104.0618-0.1917-1.76993.1217-0.87595.09680.37440.3752-0.0460.1168-0.14280.5118-0.7847-0.4189-0.6610.770.1321-0.01610.53890.01850.685234.715313.7049-24.4152
116.97191.98550.63917.05730.07555.685-0.1921-0.6988-1.05740.8673-0.00650.75920.588-0.18110.25790.73680.04780.20450.46440.12410.698269.3224-24.6997-5.9574
124.9005-1.168-0.02143.4108-1.1022.4635-0.1474-0.042-0.8680.06810.17390.806-0.2951-0.1187-0.08780.72680.06810.14690.36330.06790.661466.7209-11.6825-15.1914
132.2111-0.03932.23943.1731-1.62573.2018-0.2055-1.8605-1.10560.73270.1197-1.00430.87711.58370.05831.04910.4187-0.28592.12410.27061.347195.6997-9.58516.3708
142.50632.0991-0.63695.87951.912.6323-0.0263-0.39010.60080.38740.05790.09180.20990.68590.03330.74010.08670.0090.6840.03210.587782.4167-2.8989-3.3368
156.82621.2065-4.58882.265-0.62185.01570.24621.60210.564-0.47530.0532-0.0397-0.2784-0.8562-0.32220.77070.24470.04310.78890.1370.515787.7245-11.338-37.6586
162.617-1.490.59247.61521.32945.09130.07660.30661.8215-0.4088-0.2292-0.6414-1.3834-0.12290.22821.19890.04530.12130.62450.07171.5123108.971710.1863-36.2414
175.51991.73361.5521.95280.81741.87960.1109-0.41410.0248-0.0733-0.1603-0.5002-0.0737-0.21560.02870.91210.07750.1410.75640.02110.9119106.2013-8.1396-30.7996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:108)
2X-RAY DIFFRACTION2chain 'A' and (resseq 109:157)
3X-RAY DIFFRACTION3chain 'A' and (resseq 158:203)
4X-RAY DIFFRACTION4chain 'A' and (resseq 204:276)
5X-RAY DIFFRACTION5chain 'A' and (resseq 277:347)
6X-RAY DIFFRACTION6chain 'A' and (resseq 348:375)
7X-RAY DIFFRACTION7chain 'B' and (resseq -1:130)
8X-RAY DIFFRACTION8chain 'B' and (resseq 131:163)
9X-RAY DIFFRACTION9chain 'B' and (resseq 164:329)
10X-RAY DIFFRACTION10chain 'B' and (resseq 330:373)
11X-RAY DIFFRACTION11chain 'C' and (resseq -2:108)
12X-RAY DIFFRACTION12chain 'C' and (resseq 109:181)
13X-RAY DIFFRACTION13chain 'C' and (resseq 182:301)
14X-RAY DIFFRACTION14chain 'C' and (resseq 302:373)
15X-RAY DIFFRACTION15chain 'D' and (resseq 0:190)
16X-RAY DIFFRACTION16chain 'D' and (resseq 191:295)
17X-RAY DIFFRACTION17chain 'D' and (resseq 296:373)

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