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- PDB-6q3a: Apo form of Apolipoprotein N-acyltransferase (Lnt) -

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Basic information

Entry
Database: PDB / ID: 6q3a
TitleApo form of Apolipoprotein N-acyltransferase (Lnt)
ComponentsApolipoprotein N-acyltransferase
KeywordsMEMBRANE PROTEIN / lipoproteins / biosynthetic protein
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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWiseman, B. / Hogbom, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Sci Rep / Year: 2020
Title: Conformational changes in Apolipoprotein N-acyltransferase (Lnt).
Authors: Wiseman, B. / Hogbom, M.
History
DepositionDec 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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

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Assembly

Deposited unit
A: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9375
Polymers57,3051
Non-polymers6334
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-1 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.725, 80.725, 442.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 57304.586 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 / Plasmid: pET-28a / Production host: Escherichia coli DH1 (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41
References: UniProt: P23930, apolipoprotein N-acyltransferase
#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-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
Has ligand of interestN

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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: 3.63 Å3/Da / Density % sol: 66.14 %
Crystal growTemperature: 277 K / Method: lipidic cubic phase / pH: 7.2
Details: 36 % PEG200, 400 mM Ammonium phosphate dibasic, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→46.893 Å / Num. obs: 31865 / % possible obs: 99.6 % / Redundancy: 20.781 % / Biso Wilson estimate: 119.045 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.199 / Rrim(I) all: 0.204 / Χ2: 1.162 / Net I/σ(I): 12.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.01-3.219.6546.0940.45100058514950910.1616.25698.9
3.2-3.4121.4762.9571.04103792483348330.4963.028100
3.41-3.6922.2071.5192.31100643453245320.8141.554100
3.69-4.0421.0490.7395.4987670416541650.9660.757100
4.04-4.5120.0330.3512.9874561374037220.9910.3699.5
4.51-5.220.1180.20222.4965765330732690.9960.20798.9
5.2-6.3522.2280.16126.3762127279527950.9980.164100
6.35-8.8919.9190.08241.843902220422040.9990.085100
8.89-46.89218.8840.04465.223680127912540.9990.04698

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6L

5n6l


Resolution: 3.1→46.893 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.11
RfactorNum. reflection% reflection
Rfree0.2865 1452 4.97 %
Rwork0.2505 --
obs0.2523 29197 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 201.78 Å2 / Biso mean: 121.5941 Å2 / Biso min: 63.81 Å2
Refinement stepCycle: final / Resolution: 3.1→46.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 43 0 3914
Biso mean--130.79 --
Num. residues----492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.21080.3911430.3592764100
3.2108-3.33930.48721460.35542810100
3.3393-3.49130.3711430.32642765100
3.4913-3.67530.37791450.31232794100
3.6753-3.90540.31571460.28232749100
3.9054-4.20680.33151460.25832790100
4.2068-4.62980.2931420.2539272598
4.6298-5.29890.25661420.21192785100
5.2989-6.6730.2671540.2522785100
6.673-46.890.24091450.22372778100

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