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- PDB-8rqr: In meso structure of apolipoprotein N-acyltransferase, Lnt, from ... -

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Basic information

Entry
Database: PDB / ID: 8rqr
TitleIn meso structure of apolipoprotein N-acyltransferase, Lnt, from Escherichia coli in 7.10 monoacylglycerol
ComponentsApolipoprotein N-acyltransferase
KeywordsMEMBRANE PROTEIN / N-acyltransferase
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
: / Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsSmithers, L. / Boland, C. / Krawinski, P. / Caffrey, M.
Funding support Ireland, 4items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
Science Foundation Ireland22/FFP-A/10278 Ireland
Irish Research CouncilGOIPG/2019/3074 Ireland
Irish Research CouncilGOIPD/2021/40 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2024
Title: 7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins.
Authors: Krawinski, P. / Smithers, L. / van Dalsen, L. / Boland, C. / Ostrovitsa, N. / Perez, J. / Caffrey, M.
History
DepositionJan 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,38913
Polymers59,2811
Non-polymers3,10812
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-2 kcal/mol
Surface area22400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.679, 76.461, 157.080
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 / Copper homeostasis protein CutE


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, cutE, b0657, JW0654 / Production host: Escherichia coli (E. coli)
References: UniProt: P23930, apolipoprotein N-acyltransferase
#2: Chemical
ChemComp-A1H2K / 7.10 monoacylglycerol (S-form) / [(2S)-2,3-bis(oxidanyl)propyl] (E)-heptadec-7-enoate


Mass: 342.513 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H38O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM MES pH 6.0, 8 %(v/v) MPD, and 50-400 mM sodium or potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.19→46.5 Å / Num. obs: 30881 / % possible obs: 99.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 33.28 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.7
Reflection shellResolution: 2.19→2.27 Å / Num. unique obs: 2997 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→46.5 Å / SU ML: 0.2809 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2458 1540 5.01 %
Rwork0.1985 29200 -
obs0.2009 30740 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.62 Å2
Refinement stepCycle: LAST / Resolution: 2.19→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 216 126 4368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434352
X-RAY DIFFRACTIONf_angle_d0.79795877
X-RAY DIFFRACTIONf_chiral_restr0.0441645
X-RAY DIFFRACTIONf_plane_restr0.0091723
X-RAY DIFFRACTIONf_dihedral_angle_d12.428716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.260.36061370.32562433X-RAY DIFFRACTION92.71
2.26-2.340.30051320.28222609X-RAY DIFFRACTION99.53
2.34-2.440.32371510.25292642X-RAY DIFFRACTION99.5
2.44-2.550.29061420.23742609X-RAY DIFFRACTION99.67
2.55-2.680.28691100.22062670X-RAY DIFFRACTION99.71
2.68-2.850.2581430.20592660X-RAY DIFFRACTION99.72
2.85-3.070.26711410.20022656X-RAY DIFFRACTION99.93
3.07-3.380.24121440.18632650X-RAY DIFFRACTION99.64
3.38-3.860.24911470.17972694X-RAY DIFFRACTION99.93
3.87-4.870.19571530.16292731X-RAY DIFFRACTION99.83
4.87-46.50.20961400.1812846X-RAY DIFFRACTION98.91
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)
10.52081844141-0.118536460083-0.01984337915282.45082712558-0.3611898726070.867075828518-0.00148990167575-0.0470541416892-0.0365932502987-0.0997796603018-0.0148706732489-0.1103574464450.1624162917030.06947324863880.02662252123270.226467821773-0.00335568761652-0.002039556569320.256652798416-0.009578398245690.23324157202215.01947498613.7801389020222.0982289154
26.96684750014-2.000335260452.268357425115.011474085771.713741966634.61110311553-0.0320393717267-0.6609523819890.04362243286040.646587730134-0.00346608805910.3388247775920.055776724728-0.2266586370540.01458799724150.280994610984-0.0310661374210.01816481886730.212945232861-0.04443000654850.2074526242145.6126233083141.95551998730.0758390043
30.671621366821-0.1254102309670.02809833341911.584293012450.204533035990.9038256231340.0109676958108-0.04905434502370.05903582303380.0142374548657-0.04347119051410.20599266970.0204682623045-0.1331954968240.03480508300460.173430431192-0.0072259400838-0.01409039043680.2519713920.01092154425320.2209112131984.0273184790625.865166280219.1071231997
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 228 )-1 - 2281 - 230
22chain 'A' and (resid 229 through 277 )229 - 277231 - 277
33chain 'A' and (resid 278 through 511 )278 - 511278 - 511

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