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- PDB-5f31: Crystal structure of membrane associated PatA from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 5f31
TitleCrystal structure of membrane associated PatA from Mycobacterium smegmatis in complex with palmitate - P 42 21 2 space group
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
ETHANOL / PALMITIC ACID / Phosphatidylinositol mannoside acyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsAlbesa-Jove, D. / Svetlikova, Z. / Carreras-Gonzalez, A. / Tersa, M. / Sancho-Vaello, E. / Cifuente, J.O. / Mikusova, K. / Guerin, M.E.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis for selective recognition of acyl chains by the membrane-associated acyltransferase PatA.
Authors: Albesa-Jove, D. / Svetlikova, Z. / Tersa, M. / Sancho-Vaello, E. / Carreras-Gonzalez, A. / Bonnet, P. / Arrasate, P. / Eguskiza, A. / Angala, S.K. / Cifuente, J.O. / Kordulakova, J. / ...Authors: Albesa-Jove, D. / Svetlikova, Z. / Tersa, M. / Sancho-Vaello, E. / Carreras-Gonzalez, A. / Bonnet, P. / Arrasate, P. / Eguskiza, A. / Angala, S.K. / Cifuente, J.O. / Kordulakova, J. / Jackson, M. / Mikusova, K. / Guerin, M.E.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6244
Polymers34,2991
Non-polymers3253
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint1 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.302, 80.302, 113.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-403-

NA

21A-517-

HOH

31A-523-

HOH

41A-536-

HOH

51A-587-

HOH

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Components

#1: Protein Phosphatidylinositol mannoside acyltransferase / PIM acyltransferase


Mass: 34298.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Gene: MSMEG_2934, MSMEI_2860 / Plasmid: pJAM2::patA
Production host: Mycobacterium smegmatis str. MC2 155 (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
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl pH 8.5 and 20% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 2.43→40.19 Å / Num. obs: 14652 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 4.6
Reflection shellHighest resolution: 2.43 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→40.187 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 772 5.28 %
Rwork0.2236 --
obs0.2266 14616 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→40.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 22 87 2098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032063
X-RAY DIFFRACTIONf_angle_d0.7552806
X-RAY DIFFRACTIONf_dihedral_angle_d14.467750
X-RAY DIFFRACTIONf_chiral_restr0.041297
X-RAY DIFFRACTIONf_plane_restr0.004370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.58230.35991410.28542233X-RAY DIFFRACTION100
2.5823-2.78160.32831170.28552265X-RAY DIFFRACTION100
2.7816-3.06140.32491270.26952272X-RAY DIFFRACTION100
3.0614-3.50420.30271210.24372287X-RAY DIFFRACTION100
3.5042-4.41410.26571350.20012315X-RAY DIFFRACTION100
4.4141-40.19220.23471310.19042472X-RAY DIFFRACTION100

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