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- PDB-5vrg: Structural insights into lipoprotein N-acylation by Escherichia c... -

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Basic information

Entry
Database: PDB / ID: 5vrg
TitleStructural insights into lipoprotein N-acylation by Escherichia coli apolipoprotein N-acyltransferase
ComponentsApolipoprotein N-acyltransferase
KeywordsTRANSFERASE / Lnt / acyl transferase / membrane 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 / Apolipoprotein N-acyltransferase, N-terminal / Apolipoprotein N-acyltransferase N-terminal domain / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
PENTANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITIC ACID / Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.518 Å
AuthorsMurray, J.M. / Noland, C.L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into lipoprotein N-acylation by Escherichia coli apolipoprotein N-acyltransferase.
Authors: Noland, C.L. / Kattke, M.D. / Diao, J. / Gloor, S.L. / Pantua, H. / Reichelt, M. / Katakam, A.K. / Yan, D. / Kang, J. / Zilberleyb, I. / Xu, M. / Kapadia, S.B. / Murray, J.M.
History
DepositionMay 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)59,9499
Polymers58,2021
Non-polymers1,7468
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.764, 158.026, 44.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 58202.496 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 (E. coli)
References: UniProt: P23930, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 154 molecules

#2: 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
#3: Chemical ChemComp-LNK / PENTANE


Mass: 72.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12
#4: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5 / Details: 50 mM ADA pH 6.5 24% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.518→43.068 Å / Num. obs: 21672 / % possible obs: 98.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 32.75 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.081 / Rrim(I) all: 0.221 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)CC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
2.518-2.5267.50.7640.3520.965198
11.686-158.0265.70.9990.030.075197.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXdev_2747refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.518→43.068 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.35
RfactorNum. reflection% reflection
Rfree0.271 1100 5.13 %
Rwork0.2116 --
obs0.2147 21423 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.48 Å2 / Biso mean: 37.231 Å2 / Biso min: 16.47 Å2
Refinement stepCycle: final / Resolution: 2.518→43.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 115 146 4139
Biso mean--48.69 36.9 -
Num. residues----494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084097
X-RAY DIFFRACTIONf_angle_d1.0295555
X-RAY DIFFRACTIONf_chiral_restr0.055618
X-RAY DIFFRACTIONf_plane_restr0.008691
X-RAY DIFFRACTIONf_dihedral_angle_d13.0612419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.518-2.63260.35491000.25392383248393
2.6326-2.77140.30891500.235325272677100
2.7714-2.9450.26671360.21125382674100
2.945-3.17230.27171360.208125782714100
3.1723-3.49140.31121360.214825862722100
3.4914-3.99630.26781360.19882339247591
3.9963-5.03370.24411490.190126292778100
5.0337-43.07470.25071570.222927432900100
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)
11.93920.7205-0.05491.6956-0.01540.7691-0.0161-0.0856-0.0331-0.0442-0.0050.1310.03920.01580.00010.2566-0.00280.00870.2540.02120.2684.1332-40.1280.7113
20.7620.9282-0.10171.20430.02250.6992-0.0037-0.111-0.0739-0.0817-0.00890.02250.0138-0.01990.00010.2289-0.0054-0.0380.30220.01870.299818.8583-30.60570.6763
30.5820.2295-0.0272.3390.150.7235-0.01040.037-0.0338-0.04480.01780.2220.0194-0.13780.00090.2356-0.01160.00960.3054-0.00470.21911.2506-13.0605-6.4261
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 168 )A4 - 168
2X-RAY DIFFRACTION2chain 'A' and (resid 169 through 241 )A169 - 241
3X-RAY DIFFRACTION3chain 'A' and (resid 242 through 506 )A242 - 506

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