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- PDB-5n6m: Structure of the membrane integral lipoprotein N-acyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 5n6m
TitleStructure of the membrane integral lipoprotein N-acyltransferase Lnt from P. aeruginosa
ComponentsApolipoprotein N-acyltransferase
KeywordsMEMBRANE PROTEIN / lipoprotein / N-acyltransferase / lipidic cubic phase
Function / homology
Function and homology information


apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Apolipoprotein N-acyltransferase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
CITRATE ANION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHuang, C.-Y. / Boland, C. / Howe, N. / Wiktor, M. / Vogeley, L. / Weichert, D. / Bailey, J. / Olieric, V. / Wang, M. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Org. Science Foundation IrelandGrant number: 12/IA/1255 Ireland
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into the mechanism of the membrane integral N-acyltransferase step in bacterial lipoprotein synthesis.
Authors: Wiktor, M. / Weichert, D. / Howe, N. / Huang, C.Y. / Olieric, V. / Boland, C. / Bailey, J. / Vogeley, L. / Stansfeld, P.J. / Buddelmeijer, N. / Wang, M. / Caffrey, M.
History
DepositionFeb 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Experimental preparation / Structure summary
Category: audit_author / exptl_crystal_grow / Item: _audit_author.name / _exptl_crystal_grow.pdbx_details
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 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: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,47910
Polymers58,2301
Non-polymers2,2489
Water28816
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-0 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.730, 39.230, 102.250
Angle α, β, γ (deg.)90.00, 116.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Apolipoprotein N-acyltransferase / ALP N-acyltransferase / Copper homeostasis protein CutE homolog


Mass: 58230.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lnt, cutE, PA3984 / Cell line (production host): C41 / Production host: Pseudomonas aeruginosa (bacteria)
References: UniProt: Q9ZI86, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM NaCitrate pH 5.0 30 % (v/v) PEG-500 DME 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 3.1→49.5 Å / Num. obs: 10159 / % possible obs: 98.9 % / Redundancy: 5.4 % / Net I/σ(I): 6.48

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BUSTERrefinement
PHENIX1.10.1_2155refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6H

5n6h


Resolution: 3.1→49.5 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.84
RfactorNum. reflection% reflection
Rfree0.2729 1005 9.89 %
Rwork0.2247 --
obs0.2295 10157 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 109 16 3918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044009
X-RAY DIFFRACTIONf_angle_d0.8555455
X-RAY DIFFRACTIONf_dihedral_angle_d15.6152282
X-RAY DIFFRACTIONf_chiral_restr0.052594
X-RAY DIFFRACTIONf_plane_restr0.005683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1002-3.26370.46871540.34321296X-RAY DIFFRACTION100
3.2637-3.46810.36321310.2851284X-RAY DIFFRACTION100
3.4681-3.73580.28351520.24131294X-RAY DIFFRACTION100
3.7358-4.11160.28261320.21851310X-RAY DIFFRACTION100
4.1116-4.70610.2521410.20631292X-RAY DIFFRACTION99
4.7061-5.92760.23211470.20861315X-RAY DIFFRACTION99
5.9276-49.50.23831480.20051361X-RAY DIFFRACTION98

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