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- PDB-5f2z: Crystal structure of membrane associated PatA from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 5f2z
TitleCrystal structure of membrane associated PatA from Mycobacterium smegmatis in complex with palmitate - P21 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
PALMITIC ACID / Phosphatidylinositol mannoside acyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.2Jan 10, 2024Group: 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
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
B: Phosphatidylinositol mannoside acyltransferase
C: Phosphatidylinositol mannoside acyltransferase
D: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,2218
Polymers137,1954
Non-polymers1,0264
Water1,802100
1
A: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5552
Polymers34,2991
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5552
Polymers34,2991
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5552
Polymers34,2991
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5552
Polymers34,2991
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.830, 84.480, 98.800
Angle α, β, γ (deg.)90.00, 110.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphatidylinositol mannoside acyltransferase / PIM acyltransferase / Phosphatidyl-myo-inositol mannosides acylTransferase A (PatA)


Mass: 34298.754 Da / Num. of mol.: 4 / Fragment: UNP residues 13-304
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.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Tris-HCl pH 7.0, 230 mM MgCl2 and 12-16% (w/v) PEG 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2013
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.9→92.37 Å / Num. obs: 23420 / % possible obs: 96.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 6.6
Reflection shellHighest resolution: 2.9 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F2T

5f2t


Resolution: 2.9→92.37 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / Phase error: 30.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2737 2338 5.13 %
Rwork0.2389 --
obs0.2407 23400 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→92.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7548 0 72 100 7720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057835
X-RAY DIFFRACTIONf_angle_d0.99510710
X-RAY DIFFRACTIONf_dihedral_angle_d12.8942738
X-RAY DIFFRACTIONf_chiral_restr0.041165
X-RAY DIFFRACTIONf_plane_restr0.0051401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.95930.45251120.34632649X-RAY DIFFRACTION99
2.9593-3.02370.39611370.33162652X-RAY DIFFRACTION99
3.0237-3.0940.36871420.32232618X-RAY DIFFRACTION99
3.094-3.17140.33681360.29532603X-RAY DIFFRACTION99
3.1714-3.25710.34541450.29052599X-RAY DIFFRACTION99
3.2571-3.3530.31691380.29122624X-RAY DIFFRACTION98
3.353-3.46120.33581500.28422503X-RAY DIFFRACTION98
3.4612-3.58490.34271470.27472575X-RAY DIFFRACTION96
3.5849-3.72840.29741380.25462525X-RAY DIFFRACTION95
3.7284-3.89810.27931250.24992521X-RAY DIFFRACTION95
3.8981-4.10370.23121250.23192462X-RAY DIFFRACTION93
4.1037-4.36080.27281150.2132451X-RAY DIFFRACTION92
4.3608-4.69740.2331290.19982485X-RAY DIFFRACTION92
4.6974-5.17010.22291720.18272351X-RAY DIFFRACTION91
5.1701-5.91810.26481120.22042604X-RAY DIFFRACTION97
5.9181-7.45570.23211760.19562488X-RAY DIFFRACTION96
7.4557-92.41990.19121390.1842557X-RAY DIFFRACTION96

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