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- PDB-5f34: Crystal structure of membrane associated PatA from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 5f34
TitleCrystal structure of membrane associated PatA from Mycobacterium smegmatis in complex with S-hexadecyl Coenzyme A - 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
Chem-HD6 / Phosphatidylinositol mannoside acyltransferase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.281 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)141,1638
Polymers137,1954
Non-polymers3,9684
Water41423
1
A: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2912
Polymers34,2991
Non-polymers9921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2912
Polymers34,2991
Non-polymers9921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2912
Polymers34,2991
Non-polymers9921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2912
Polymers34,2991
Non-polymers9921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.080, 80.270, 97.380
Angle α, β, γ (deg.)90.00, 110.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphatidylinositol mannoside acyltransferase / PIM acyltransferase


Mass: 34298.754 Da / Num. of mol.: 4
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-HD6 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S})-4-[[3-(2-hexadecylsulfanylethylamino)-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate


Mass: 991.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H68N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 500 mM ammonium sulfate and 30% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2015
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR i03 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.28→47.12 Å / Num. obs: 17931 / % possible obs: 99.13 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.18
Reflection shellHighest resolution: 3.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.47 / % possible all: 94.36

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F2T

5f2t


Resolution: 3.281→47.116 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.306 931 5.2 %
Rwork0.264 --
obs0.2662 17906 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.281→47.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7400 0 174 23 7597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047791
X-RAY DIFFRACTIONf_angle_d1.08410682
X-RAY DIFFRACTIONf_dihedral_angle_d14.3932748
X-RAY DIFFRACTIONf_chiral_restr0.0451165
X-RAY DIFFRACTIONf_plane_restr0.0051394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2809-3.45390.43161430.38922307X-RAY DIFFRACTION96
3.4539-3.67020.35081270.31462439X-RAY DIFFRACTION99
3.6702-3.95340.32911250.29692405X-RAY DIFFRACTION100
3.9534-4.3510.28661200.26182455X-RAY DIFFRACTION100
4.351-4.980.28591440.24072432X-RAY DIFFRACTION100
4.98-6.2720.32011510.26982427X-RAY DIFFRACTION99
6.272-47.12080.26871210.23062510X-RAY DIFFRACTION99

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