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Basic information

Entry
Database: PDB / ID: 5oce
TitleTHE MOLECULAR MECHANISM OF SUBSTRATE RECOGNITION AND CATALYSIS OF THE MEMBRANE ACYLTRANSFERASE PatA -- Complex of PatA with palmitate, mannose, and palmitoyl-6-mannose
ComponentsPhosphatidylinositol mannoside acyltransferase
KeywordsTRANSFERASE / acyltransferase / glycolipid biosynthesis
Function / homology
Function and homology information


phosphatidylinositol dimannoside acyltransferase / glycolipid biosynthetic process / phosphatidylinositol metabolic process / phospholipid biosynthetic process / acyltransferase activity / plasma membrane
Similarity search - Function
Bacterial lipid A biosynthesis acyltransferase / Bacterial lipid A biosynthesis acyltransferase
Similarity search - Domain/homology
Chem-9R2 / beta-D-mannopyranose / PALMITIC ACID / Phosphatidylinositol mannoside acyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsAlbesa-Jove, D. / Tersa, M. / Guerin, M.E.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: The Molecular Mechanism of Substrate Recognition and Catalysis of the Membrane Acyltransferase PatA from Mycobacteria.
Authors: Tersa, M. / Raich, L. / Albesa-Jove, D. / Trastoy, B. / Prandi, J. / Gilleron, M. / Rovira, C. / Guerin, M.E.
History
DepositionJun 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol mannoside acyltransferase
B: Phosphatidylinositol mannoside acyltransferase
C: Phosphatidylinositol mannoside acyltransferase
D: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,0579
Polymers134,3644
Non-polymers1,6925
Water2,612145
1
A: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0283
Polymers33,5911
Non-polymers4372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0102
Polymers33,5911
Non-polymers4191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0102
Polymers33,5911
Non-polymers4191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0102
Polymers33,5911
Non-polymers4191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.690, 83.860, 98.430
Angle α, β, γ (deg.)90.00, 110.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphatidylinositol mannoside acyltransferase / PIM acyltransferase


Mass: 33591.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: MSMEG_2934, MSMEI_2860 / Production host: Mycobacterium smegmatis (bacteria)
References: UniProt: A0QWG5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-9R2 / [(2~{R},3~{S},4~{S},5~{S},6~{S})-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hexadecanoate


Mass: 418.565 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H42O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: The crystal of PatA was obtained by mixing 0.25ul of the protein (5 mg ml-1) in 5 mM D-(+)-mannose and 20 mM Tris-HCl buffer pH 7.5 with 0.25ul of a mother liquor containing, 100 mM Tris-HCl ...Details: The crystal of PatA was obtained by mixing 0.25ul of the protein (5 mg ml-1) in 5 mM D-(+)-mannose and 20 mM Tris-HCl buffer pH 7.5 with 0.25ul of a mother liquor containing, 100 mM Tris-HCl pH 7.0, 225 mM MgCl2 and 16% (w/v) PEG 8,000.
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.41→28.77 Å / Num. obs: 40218 / % possible obs: 97.17 % / Redundancy: 3.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1125 / Net I/σ(I): 12.76
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.4939 / Num. unique obs: 3754 / CC1/2: 0.773 / % possible all: 90.55

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Processing

Software
NameVersionClassification
PHENIX(dev_2219)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F2T

5f2t


Resolution: 2.41→28.77 Å / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 22.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 2049 5.09 %Random
Rwork0.1817 ---
obs0.1887 40218 97.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.52 Å2
Refinement stepCycle: LAST / Resolution: 2.41→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7808 0 117 145 8070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028163
X-RAY DIFFRACTIONf_angle_d0.56111131
X-RAY DIFFRACTIONf_dihedral_angle_d17.3014822
X-RAY DIFFRACTIONf_chiral_restr0.0381192
X-RAY DIFFRACTIONf_plane_restr0.0031460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4184-2.47880.32151420.27632597X-RAY DIFFRACTION89
2.4788-2.54580.26161400.26352738X-RAY DIFFRACTION93
2.5458-2.62060.29711440.26612719X-RAY DIFFRACTION93
2.6206-2.70510.26351410.25322721X-RAY DIFFRACTION93
2.7051-2.80170.26241440.24142734X-RAY DIFFRACTION93
2.8017-2.91380.25411390.232714X-RAY DIFFRACTION94
2.9138-3.04630.24691460.22172766X-RAY DIFFRACTION93
3.0463-3.20670.21691380.21362728X-RAY DIFFRACTION93
3.2067-3.40730.23411430.21172712X-RAY DIFFRACTION92
3.4073-3.66980.22921450.19342703X-RAY DIFFRACTION92
3.6698-4.03810.19971460.16782733X-RAY DIFFRACTION93
4.0381-4.62020.20651450.14592727X-RAY DIFFRACTION93
4.6202-5.81240.16671440.13672777X-RAY DIFFRACTION93
5.8124-280.18861480.15552824X-RAY DIFFRACTION93

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