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- PDB-5n6h: Structure of the membrane integral lipoprotein N-acyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 5n6h
TitleStructure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli
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 / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
Apolipoprotein N-acyltransferase, N-terminal / Apolipoprotein N-acyltransferase N-terminal domain / Apolipoprotein N-acyltransferase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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 Ireland12/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 / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein N-acyltransferase
B: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,17633
Polymers118,5622
Non-polymers7,61531
Water45025
1
A: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,20420
Polymers59,2811
Non-polymers4,92319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,97313
Polymers59,2811
Non-polymers2,69212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.200, 142.300, 199.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 59280.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lnt, cutE, b0657, JW0654 / Cell (production host): C43 / Production host: Escherichia coli (E. coli)
References: UniProt: P23930, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.38 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 8 % (v/v) MPD 0.1 MES pH 6.0 0.4 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 7, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.9→49.1 Å / Num. obs: 693957 / % possible obs: 100 % / Redundancy: 19.6 % / Net I/σ(I): 9.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
BUSTERrefinement
PHENIX(1.10.1_2155: ???)refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.9→49.099 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7
RfactorNum. reflection% reflection
Rfree0.2494 1763 5 %
Rwork0.2189 --
obs0.2204 35266 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7862 0 395 25 8282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038452
X-RAY DIFFRACTIONf_angle_d0.72811429
X-RAY DIFFRACTIONf_dihedral_angle_d15.1274918
X-RAY DIFFRACTIONf_chiral_restr0.0491268
X-RAY DIFFRACTIONf_plane_restr0.0051415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97840.3811340.34112555X-RAY DIFFRACTION100
2.9784-3.0660.36951320.31682508X-RAY DIFFRACTION100
3.066-3.1650.32371350.29292548X-RAY DIFFRACTION100
3.165-3.27810.32721320.2792518X-RAY DIFFRACTION100
3.2781-3.40930.27791350.26332562X-RAY DIFFRACTION100
3.4093-3.56440.27451340.26012541X-RAY DIFFRACTION100
3.5644-3.75230.32631330.25132531X-RAY DIFFRACTION100
3.7523-3.98730.23261360.20932578X-RAY DIFFRACTION100
3.9873-4.2950.21821340.20322553X-RAY DIFFRACTION100
4.295-4.72690.22021360.19032587X-RAY DIFFRACTION100
4.7269-5.41010.24041380.18852623X-RAY DIFFRACTION100
5.4101-6.81330.22291390.21182635X-RAY DIFFRACTION100
6.8133-49.10610.22411450.19552764X-RAY DIFFRACTION100

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