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- PDB-5kn7: Lipid A secondary acyltransferase LpxM from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 5kn7
TitleLipid A secondary acyltransferase LpxM from Acinetobacter baumannii
ComponentsLipid A biosynthesis lauroyl acyltransferase
KeywordsTRANSFERASE / LpxM MsbB WaaN / Acyl Transferase / Lauryl Transferase
Function / homologyBacterial lipid A biosynthesis acyltransferase / Bacterial lipid A biosynthesis acyltransferase / glycolipid biosynthetic process / acyltransferase activity / plasma membrane / PHOSPHATE ION / Lipid A biosynthesis lauroyl acyltransferase
Function and homology information
Biological speciesAcinetobacter baumannii NIPH 410 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsDovala, D.L. / Hu, Q. / Metzger IV, L.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure-guided enzymology of the lipid A acyltransferase LpxM reveals a dual activity mechanism.
Authors: Dovala, D. / Rath, C.M. / Hu, Q. / Sawyer, W.S. / Shia, S. / Elling, R.A. / Knapp, M.S. / Metzger, L.E.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Oct 26, 2016Group: Database references
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Lipid A biosynthesis lauroyl acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,89117
Polymers38,1921
Non-polymers1,69916
Water2,720151
1
B: Lipid A biosynthesis lauroyl acyltransferase
hetero molecules

B: Lipid A biosynthesis lauroyl acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,78234
Polymers76,3832
Non-polymers3,39932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area11880 Å2
ΔGint-186 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.770, 145.330, 87.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-622-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules B

#1: Protein Lipid A biosynthesis lauroyl acyltransferase


Mass: 38191.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii NIPH 410 (bacteria)
Gene: F910_00940 / Production host: Escherichia coli (E. coli) / References: UniProt: S3TFW2
#5: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 166 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.55 Å3/Da / Density % sol: 51.84 % / Description: Small guitar-pick shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM NaBr 2.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2015
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→72.67 Å / Num. obs: 26054 / % possible obs: 99.9 % / Redundancy: 2 % / Net I/σ(I): 9.02

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→72.665 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1
RfactorNum. reflection% reflection
Rfree0.267 1043 4.03 %
Rwork0.2127 --
obs0.2149 25885 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.72 Å2 / Biso mean: 43.2784 Å2 / Biso min: 18.28 Å2
Refinement stepCycle: final / Resolution: 1.99→72.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 106 151 2747
Biso mean--60.16 44.99 -
Num. residues----319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092671
X-RAY DIFFRACTIONf_angle_d0.9713627
X-RAY DIFFRACTIONf_chiral_restr0.054412
X-RAY DIFFRACTIONf_plane_restr0.006451
X-RAY DIFFRACTIONf_dihedral_angle_d14.2391578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.0950.38621470.30153492363999
2.095-2.22620.32741460.27543475362199
2.2262-2.39810.32931460.24443517366399
2.3981-2.63950.27981480.2335273675100
2.6395-3.02140.29861500.22583539368999
3.0214-3.80670.2541510.196435873738100
3.8067-72.71350.22861550.18983705386099

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