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- PDB-6nwr: Thioester acyl-intermediate of Apolipoprotein N-acyltransferase (Lnt) -

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Basic information

Entry
Database: PDB / ID: 6nwr
TitleThioester acyl-intermediate of Apolipoprotein N-acyltransferase (Lnt)
Components(Apolipoprotein N-acyltransferase) x 2
KeywordsMEMBRANE PROTEIN / Enzyme / Nitrilase / N-acyltransferase / Lipoprotein
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 domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DODECANE / Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 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
DepositionFeb 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
B: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9176
Polymers118,2152
Non-polymers1,7024
Water00
1
A: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4992
Polymers58,9881
Non-polymers5111
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4184
Polymers59,2271
Non-polymers1,1923
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.164, 136.989, 220.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 58988.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lnt, cutE, b0657, JW0654 / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): C41
References: UniProt: P23930, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein Apolipoprotein N-acyltransferase / ALP N-acyltransferase / Copper homeostasis protein CutE


Mass: 59226.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lnt, cutE, b0657, JW0654 / Production host: Escherichia coli DH5[alpha] (bacteria) / Strain (production host): C41
References: UniProt: P23930, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26

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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: 4.63 Å3/Da / Density % sol: 73.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 25 % PEG 2000MME, 100 mM Na cacodylate, 40 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→48.47 Å / Num. obs: 28448 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.277 / Net I/σ(I): 5.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
3.5-3.717.22.35845080.4331100
10.5-48.476.70.0911690.997199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.3data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6L

5n6l


Resolution: 3.5→48.469 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 28.2
RfactorNum. reflection% reflection
Rfree0.2749 2591 4.87 %
Rwork0.2593 --
obs0.26 28382 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 215.04 Å2 / Biso mean: 109.6441 Å2 / Biso min: 36.96 Å2
Refinement stepCycle: final / Resolution: 3.5→48.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7885 0 103 0 7988
Biso mean--162.89 --
Num. residues----999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.5-3.56360.33171360.358626672803
3.5636-3.63220.30241280.344426702798
3.6322-3.70630.3531420.336826502792
3.7063-3.78680.36531410.326926822823
3.7868-3.87490.32371310.322626582789
3.8749-3.97180.34341510.296926782829
3.9718-4.07910.27521390.281926662805
4.0791-4.19910.30551380.265626372775
4.1991-4.33450.27751150.260926982813
4.3345-4.48930.2731430.237426702813
4.4893-4.66890.21411600.228726032763
4.6689-4.88120.24421190.211426992818
4.8812-5.13830.24681540.224626672821
5.1383-5.45980.22771470.217626312778
5.4598-5.88070.26651190.228826732792
5.8807-6.47130.24731340.22626992833
6.4713-7.40480.22041280.218126542782
7.4048-9.31850.21611340.213526752809
9.3185-48.47340.32051320.289526732805

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