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- PDB-5knk: Lipid A secondary acyltransferase LpxM from Acinetobacter baumann... -

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Basic information

Entry
Database: PDB / ID: 5knk
TitleLipid A secondary acyltransferase LpxM from Acinetobacter baumannii with catalytic residue substitution (E127A)
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 / UNDECANOIC ACID / Lipid A biosynthesis lauroyl acyltransferase
Function and homology information
Biological speciesAcinetobacter baumannii NIPH 410 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 28, 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 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Lipid A biosynthesis lauroyl acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,00211
Polymers38,1341
Non-polymers1,86810
Water1,892105
1
B: Lipid A biosynthesis lauroyl acyltransferase
hetero molecules

B: Lipid A biosynthesis lauroyl acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,00322
Polymers76,2672
Non-polymers3,73620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area13390 Å2
ΔGint-158 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.300, 145.470, 87.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 3 molecules B

#1: Protein Lipid A biosynthesis lauroyl acyltransferase


Mass: 38133.590 Da / Num. of mol.: 1 / Mutation: E127A
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
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 113 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-11A / UNDECANOIC ACID


Mass: 186.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.56 Å3/Da / Density % sol: 51.94 % / Description: Small guitar pick shaped crystals.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM KBr 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: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→72.74 Å / Num. obs: 30262 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.998 / Net I/σ(I): 7.95

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KN7

5kn7


Resolution: 1.9→72.735 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.79
RfactorNum. reflection% reflection
Rfree0.2712 871 2.88 %
Rwork0.2252 --
obs0.2265 30262 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.9 Å2 / Biso mean: 32.284 Å2 / Biso min: 10.68 Å2
Refinement stepCycle: final / Resolution: 1.9→72.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 121 105 2792
Biso mean--42.52 33.33 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072804
X-RAY DIFFRACTIONf_angle_d1.13806
X-RAY DIFFRACTIONf_chiral_restr0.061433
X-RAY DIFFRACTIONf_plane_restr0.005470
X-RAY DIFFRACTIONf_dihedral_angle_d17.5991682
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9001-2.01920.37831420.308848224964
2.0192-2.17510.30231440.257448404984
2.1751-2.3940.32391440.250248575001
2.394-2.74040.31291440.226948665010
2.7404-3.45260.25931460.218449195065
3.4526-72.78830.22641510.201750875238

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