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- PDB-8q2p: Structure of the membrane integral lipoprotein N-acyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 8q2p
TitleStructure of the membrane integral lipoprotein N-acyltransferase Lnt from E. coli by using Se-MAG for the the lipid cubic phase crystallization
ComponentsApolipoprotein N-acyltransferase
KeywordsTRANSFERASE / co-crystallization / experimental phasing / lipoprotein N-acyltransferase / selenium-sulfur hydrogen bond / seleno-monoacylglyceride / X-ray scattering
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 / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
: / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHuang, C.-Y. / Boland, C. / Kaki, S.S. / Wang, M. / Olieric, V. / Caffrey, M.
Funding supportEuropean Union, Ireland, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission701647European Union
Science Foundation Ireland16/IA/4435 Ireland
CitationJournal: Crystals / Year: 2023
Title: Se-MAG Is a Convenient Additive for Experimental Phasing and Structure Determination of Membrane Proteins Crystallised by the Lipid Cubic Phase (In Meso) Method
Authors: Boland, C. / Huang, C.Y. / Shanker Kaki, S. / Wang, M. / Olieric, V. / Caffrey, M.
History
DepositionAug 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,70127
Polymers56,8231
Non-polymers7,87826
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-1 kcal/mol
Surface area21990 Å2
Unit cell
Length a, b, c (Å)156.610, 48.790, 75.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 56823.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lnt, cutE, b0657, JW0654 / Production host: Escherichia coli (E. coli)
References: UniProt: P23930, apolipoprotein N-acyltransferase

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Non-polymers , 5 types, 328 molecules

#2: Chemical
ChemComp-IRY / [(2~{S})-2,3-bis(oxidanyl)propyl] 8-hexylselanyloctanoate


Mass: 381.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C17H34O4Se / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 0.1 M MES-NaOH pH 6.0, 8 %(v/v) MPD, and 0.4 M sodium or potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97939 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.9→43.02 Å / Num. obs: 87726 / % possible obs: 99 % / Redundancy: 80.88 % / Biso Wilson estimate: 27.21 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.31 / Net I/σ(I): 19.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.28 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 6484 / CC1/2: 0.99 / Rrim(I) all: 2.95 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSVERSION Feb 5, 2021 BUILT=20210323data reduction
XSCALEVERSION Feb 5, 2021 BUILT=20210323data scaling
SHELXCDVersion 2016/1phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→43.02 Å / SU ML: 0.2201 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2236 2321 5 %
Rwork0.1843 44101 -
obs0.1863 46422 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.28 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 164 302 4760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434654
X-RAY DIFFRACTIONf_angle_d0.82056209
X-RAY DIFFRACTIONf_chiral_restr0.0487666
X-RAY DIFFRACTIONf_plane_restr0.0071745
X-RAY DIFFRACTIONf_dihedral_angle_d29.7366914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.41771330.39882530X-RAY DIFFRACTION99.03
1.94-1.980.26171350.2442563X-RAY DIFFRACTION100
1.98-2.030.26261370.20382611X-RAY DIFFRACTION100
2.03-2.080.26111340.19382545X-RAY DIFFRACTION100
2.08-2.130.24261370.18542594X-RAY DIFFRACTION100
2.13-2.20.24031360.17642583X-RAY DIFFRACTION100
2.2-2.270.55631170.3332252X-RAY DIFFRACTION87.32
2.27-2.350.21151370.17062602X-RAY DIFFRACTION100
2.35-2.440.21091380.16282614X-RAY DIFFRACTION100
2.44-2.550.17631350.1562571X-RAY DIFFRACTION100
2.55-2.690.17751380.15722610X-RAY DIFFRACTION100
2.69-2.860.22361370.1592611X-RAY DIFFRACTION100
2.86-3.080.19241380.16772626X-RAY DIFFRACTION100
3.08-3.390.18211380.16542619X-RAY DIFFRACTION100
3.39-3.880.20521400.17252650X-RAY DIFFRACTION99.68
3.88-4.880.21331420.16342705X-RAY DIFFRACTION99.93
4.88-43.020.21191490.20082815X-RAY DIFFRACTION99.76

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