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- PDB-7aci: In meso structure of apolipoprotein N-acyltransferase, Lnt, from ... -

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Basic information

Entry
Database: PDB / ID: 7aci
TitleIn meso structure of apolipoprotein N-acyltransferase, Lnt, from Escherichia coli in 9.8 monoacylglycerol
ComponentsApolipoprotein N-acyltransferase
KeywordsMEMBRANE PROTEIN / Nitrilase fold / helical bundle
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
Chem-LH9 / Apolipoprotein N-acyltransferase / Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSmithers, L. / van Dalsen, L. / Boland, C. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland Ireland
CitationJournal: Cryst.Growth Des. / Year: 2020
Title: 9.8 MAG. A new host lipid for in meso (lipid cubic phase) crystallization of integral membrane proteins
Authors: van Dalsen, L. / Smithers, L. / Boland, C. / Weichert, D. / Caffrey, M.
History
DepositionSep 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)61,88813
Polymers59,2811
Non-polymers2,60812
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.775, 76.173, 156.531
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Apolipoprotein N-acyltransferase / ALP N-acyltransferase


Mass: 59280.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: lnt, ACU57_00505, AM464_20560, AUQ13_21565, BMA87_17500, BUE81_17200, BvCms2454_02009, BvCmsHHP001_00880, BvCmsKSNP120_02778, BvCmsKSP076_04015, BW690_14780, C5N07_14455, C9Z39_12310, CA593_ ...Gene: lnt, ACU57_00505, AM464_20560, AUQ13_21565, BMA87_17500, BUE81_17200, BvCms2454_02009, BvCmsHHP001_00880, BvCmsKSNP120_02778, BvCmsKSP076_04015, BW690_14780, C5N07_14455, C9Z39_12310, CA593_25875, CI694_20445, CIG45_13010, D0X26_17735, D2185_16075, D3821_19610, D4638_22450, D4718_15390, D9D20_13050, D9D44_16075, D9G69_11750, D9J52_13020, DBQ99_18215, DJ503_07085, DL326_16140, DT034_15925, E2119_09030, E4K55_13820, E4K60_15665, E4K61_12850, EA213_10835, EAI52_07270, EC3234A_6c00760, EC3426_01483, ECTO6_03389, ED307_12710, EEP23_08605, EI021_13075, EI028_12695, EI041_12995, EIZ93_02940, EL75_3125, EL79_3219, EL80_3175, ELT20_10985, EPT01_08450, EXX71_13910, EYD11_16175, FV293_12780, GHR40_20735, GKF74_06475, GKF86_07920, GKF89_05980, GP689_15750, GQE34_06850, GQM17_21560, GRW42_10840, NCTC8500_03946, NCTC9045_04089, NCTC9062_04723, NCTC9969_03714, PGD_02673, RK56_025370, SAMEA3472047_02047, SAMEA3472080_00307, SAMEA3484427_03116, SAMEA3484429_03266, SAMEA3752559_01009, SAMEA3753300_04108, SK85_00657
Production host: Escherichia coli (E. coli)
References: UniProt: A0A037YBN4, UniProt: P23930*PLUS, apolipoprotein N-acyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-LH9 / [(2~{S})-2,3-bis(oxidanyl)propyl] heptadec-9-enoate


Mass: 342.513 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H38O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1M MES pH 6.0, * %(v/v) MPD, 0.05-0.4 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.3→46.57 Å / Num. obs: 26629 / % possible obs: 99.34 % / Redundancy: 12.9 % / Biso Wilson estimate: 38.94 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 2578 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Coot1.17.1_3660model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6H

5n6h


Resolution: 2.3→46.57 Å / SU ML: 0.2367 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 1423 5.36 %
Rwork0.2143 25142 -
obs0.2167 26565 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 180 73 4213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414259
X-RAY DIFFRACTIONf_angle_d0.6355766
X-RAY DIFFRACTIONf_chiral_restr0.0422638
X-RAY DIFFRACTIONf_plane_restr0.0038714
X-RAY DIFFRACTIONf_dihedral_angle_d15.5445677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.33991140.26672500X-RAY DIFFRACTION99.17
2.38-2.480.30051460.25982436X-RAY DIFFRACTION99.38
2.48-2.590.31331260.25352500X-RAY DIFFRACTION99.58
2.59-2.730.31451560.2392485X-RAY DIFFRACTION99.66
2.73-2.90.26331530.22962472X-RAY DIFFRACTION99.81
2.9-3.120.25441370.21632513X-RAY DIFFRACTION99.85
3.12-3.440.23771340.20682485X-RAY DIFFRACTION98.53
3.44-3.930.25671490.22252516X-RAY DIFFRACTION99.11
3.93-4.950.23421460.19082577X-RAY DIFFRACTION99.89
4.95-46.570.24321620.19782658X-RAY DIFFRACTION98.6
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1569236533880.158959491748-0.0135876906740.557577049764-0.4181633005280.4076219416140.02841896336810.0163604796169-0.0637169005353-0.02316762153940.0374653223882-0.07315982270170.108242539270.0183159711656-4.18206058985E-70.346256273116-0.0072110275050.001586509089410.325445874609-0.008999603264630.34666108565812.86777119592.0213342975624.4994077924
20.4536287093910.136379050480.00299166120860.58275250697-0.289766829490.4509969034580.04569041535940.02567214256580.140739843707-0.0207588358154-0.103869923680.0446001013372-0.0682692774615-0.1306061648340.0001836038585010.284954972102-0.02526122718360.002777441987480.323558147536-0.002597674684640.2907129516888.0911889148333.355200139920.3501797373
30.04041121459050.136684606780.1294000378460.675574165590.3090951234250.2463775326890.01577994314140.02147254273730.08960642319340.087717616677-0.02984201393650.01489274098340.0288305024574-0.01411042204179.050365951E-50.29499455893-0.00247376332312-0.004671942368190.3765774602190.01995897565840.3190028458015.7702624293223.302171983718.3055455066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 189 )
2X-RAY DIFFRACTION2chain 'A' and (resid 190 through 320 )
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 508 )

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