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- PDB-5vrh: Apolipoprotein N-acyltransferase C387S active site mutant -

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Basic information

Entry
Database: PDB / ID: 5vrh
TitleApolipoprotein N-acyltransferase C387S active site mutant
ComponentsApolipoprotein N-acyltransferase
KeywordsTRANSFERASE / Lnt C387S / 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, 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
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (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 / molecular replacement / Resolution: 2.137 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 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1859
Polymers58,1861
Non-polymers1,9998
Water4,648258
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)52.671, 72.586, 75.610
Angle α, β, γ (deg.)90.000, 101.730, 90.000
Int Tables number4
Space group name H-MP1211

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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: 58186.441 Da / Num. of mol.: 1 / Mutation: C387S
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 , 6 types, 266 molecules

#2: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.7
Details: 0.1 M MES pH 5.7 - 6.3, 27% PEG 500 DME, 0.1 M sodium chloride, 0.1 M magnesium chloride, and 0.01 M copper(II) chloride dihydrate
PH range: 5.7 - 6.3

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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: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.137→42.041 Å / Num. obs: 30232 / % possible obs: 97.4 % / Redundancy: 5 % / Biso Wilson estimate: 27.6 Å2 / CC1/2: 0.973 / Rpim(I) all: 0.071 / Rrim(I) all: 0.159 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)CC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
2.137-2.1444.60.7070.3850.84194.5
9.912-72.5864.80.8620.0360.071100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIXdev_2747refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 5VRG

5vrg


Resolution: 2.137→42.041 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.97
RfactorNum. reflection% reflection
Rfree0.2501 1461 4.84 %
Rwork0.2066 --
obs0.2086 30207 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.48 Å2 / Biso mean: 33.8879 Å2 / Biso min: 14.2 Å2
Refinement stepCycle: final / Resolution: 2.137→42.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 138 258 4238
Biso mean--57.46 43.05 -
Num. residues----490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024091
X-RAY DIFFRACTIONf_angle_d0.6485548
X-RAY DIFFRACTIONf_chiral_restr0.042614
X-RAY DIFFRACTIONf_plane_restr0.005688
X-RAY DIFFRACTIONf_dihedral_angle_d9.613305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1372-2.21360.29761530.29272886303999
2.2136-2.30220.31951610.256429513112100
2.3022-2.4070.30891270.244829253052100
2.407-2.53390.28071710.235529173088100
2.5339-2.69260.29821260.22262516264285
2.6926-2.90050.27751380.21229663104100
2.9005-3.19230.24841500.206229363086100
3.1923-3.6540.23521420.18562871301397
3.654-4.60270.2211390.17692757289693
4.6027-42.0490.21091540.188730213175100
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)
11.1142-0.22530.12531.0582-0.0461.73350.0281-0.1269-0.11990.1923-0.02550.03240.10890.0656-0.00010.2247-0.02420.0030.18950.02450.2007-12.1768-1.7006-1.6683
20.32330.06560.32710.6331-0.1990.97970.0321-0.0650.01470.02580.00170.0657-0.1327-0.0748-00.1727-0.00820.00020.1765-0.00810.2488-19.71277.0878-14.9569
30.87680.0413-0.121.11560.62582.21340.03850.1047-0.0669-0.06240.0286-0.2-0.02820.26510.00720.1714-0.0214-0.00170.21170.00130.2314-5.81033.967-29.5616
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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