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- PDB-5n6l: Structure of the membrane integral lipoprotein N-acyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 5n6l
TitleStructure of the membrane integral lipoprotein N-acyltransferase Lnt C387A mutant from E. coli
ComponentsApolipoprotein N-acyltransferase
KeywordsTRANSFERASE / membrane 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 / Apolipoprotein N-acyltransferase, N-terminal / Apolipoprotein N-acyltransferase N-terminal domain / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
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 / MOLECULAR REPLACEMENT / 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
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
B: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,22941
Polymers118,4972
Non-polymers10,73239
Water23413
1
A: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,76028
Polymers59,2491
Non-polymers7,51127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,46913
Polymers59,2491
Non-polymers3,22112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.220, 142.950, 197.710
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: 59248.695 Da / Num. of mol.: 2 / Mutation: C387A
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.: 27 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 8 % (v/v) MPD 0.1 M MES pH 6 0.4 M ammonium citrate 0.1 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.9→49.79 Å / Num. obs: 34916 / % possible obs: 97.9 % / Redundancy: 5.4 % / Net I/σ(I): 7.72

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BUSTERrefinement
PHENIX(1.10.1_2155: ???)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6H

5n6h


Resolution: 2.9→49.79 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.36
RfactorNum. reflection% reflection
Rfree0.2633 1699 4.88 %
Rwork0.2271 --
obs0.2288 34807 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7845 0 513 13 8371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048543
X-RAY DIFFRACTIONf_angle_d0.79811524
X-RAY DIFFRACTIONf_dihedral_angle_d14.4244955
X-RAY DIFFRACTIONf_chiral_restr0.051272
X-RAY DIFFRACTIONf_plane_restr0.0061423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.98530.40791230.33862348X-RAY DIFFRACTION86
2.9853-3.08170.38741300.35072533X-RAY DIFFRACTION91
3.0817-3.19180.31691390.31962782X-RAY DIFFRACTION100
3.1918-3.31960.3551420.3062783X-RAY DIFFRACTION100
3.3196-3.47060.3041440.28072802X-RAY DIFFRACTION100
3.4706-3.65350.33171350.2692797X-RAY DIFFRACTION100
3.6535-3.88240.28421540.2452757X-RAY DIFFRACTION99
3.8824-4.1820.25591450.22082808X-RAY DIFFRACTION100
4.182-4.60260.27111400.22152793X-RAY DIFFRACTION98
4.6026-5.26790.23311570.19252800X-RAY DIFFRACTION99
5.2679-6.63460.2521550.21322868X-RAY DIFFRACTION100
6.6346-49.85380.20071350.18323037X-RAY DIFFRACTION99

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