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- PDB-5f2t: Crystal structure of membrane associated PatA from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 5f2t
TitleCrystal structure of membrane associated PatA from Mycobacterium smegmatis in complex with palmitate - C 2 space group
ComponentsPhosphatidylinositol mannoside acyltransferase
KeywordsTRANSFERASE / acyltransferase / glycolipid biosynthesis
Function / homology
Function and homology information


phosphatidylinositol dimannoside acyltransferase / glycolipid biosynthetic process / phospholipid biosynthetic process / phosphatidylinositol metabolic 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1355
Polymers68,5982
Non-polymers5373
Water6,287349
1
A: Phosphatidylinositol mannoside acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5793
Polymers34,2991
Non-polymers2812
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
Unit cell
Length a, b, c (Å)93.600, 71.090, 76.250
Angle α, β, γ (deg.)90.00, 91.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-645-

HOH

21A-685-

HOH

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Components

#1: Protein Phosphatidylinositol mannoside acyltransferase / PIM acyltransferase


Mass: 34298.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (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.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 1.85 Å3/Da / Density % sol: 33.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting 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, 2015
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: 2.06→56.6 Å / Num. obs: 30533 / % possible obs: 98.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.6
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 86.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→56.601 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 3025 5.06 %
Rwork0.1732 --
obs0.1761 30529 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→56.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 37 349 4368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044211
X-RAY DIFFRACTIONf_angle_d0.7685740
X-RAY DIFFRACTIONf_dihedral_angle_d17.8382497
X-RAY DIFFRACTIONf_chiral_restr0.177602
X-RAY DIFFRACTIONf_plane_restr0.004764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.09220.32971140.27442233X-RAY DIFFRACTION84
2.0922-2.12650.33211270.25442381X-RAY DIFFRACTION91
2.1265-2.16320.32131050.24712561X-RAY DIFFRACTION95
2.1632-2.20250.29361280.24092578X-RAY DIFFRACTION100
2.2025-2.24490.29621530.22122606X-RAY DIFFRACTION100
2.2449-2.29070.28811380.20942568X-RAY DIFFRACTION100
2.2907-2.34050.23811560.18882657X-RAY DIFFRACTION100
2.3405-2.3950.24831480.18522551X-RAY DIFFRACTION100
2.395-2.45480.24671440.1792703X-RAY DIFFRACTION100
2.4548-2.52120.21841310.1782555X-RAY DIFFRACTION100
2.5212-2.59540.22371290.17272615X-RAY DIFFRACTION100
2.5954-2.67920.24851330.16982669X-RAY DIFFRACTION100
2.6792-2.77490.27781110.17992637X-RAY DIFFRACTION100
2.7749-2.8860.28191460.17392601X-RAY DIFFRACTION100
2.886-3.01740.22411110.16722609X-RAY DIFFRACTION100
3.0174-3.17640.271220.16012655X-RAY DIFFRACTION100
3.1764-3.37540.21451400.15832628X-RAY DIFFRACTION100
3.3754-3.6360.22411470.14472623X-RAY DIFFRACTION100
3.636-4.00180.18351820.13872549X-RAY DIFFRACTION100
4.0018-4.58070.18161410.13832607X-RAY DIFFRACTION100
4.5807-5.77030.17641280.15312655X-RAY DIFFRACTION100
5.7703-56.62190.23061910.2082554X-RAY DIFFRACTION99

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