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- PDB-6hy2: Structure guided design of an antibacterial peptide that targets ... -

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Basic information

Entry
Database: PDB / ID: 6hy2
TitleStructure guided design of an antibacterial peptide that targets UDP-N-acetylglucosamine acyltransferase
Components
  • Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
  • TRP-MET-LEU-ASP-PRO-ILE-ALA-GLY-LYS-TRP-SER-ARG
KeywordsTRANSFERASE / LpxA / antibiotics / inhibitor / acyltransferase
Function / homology
Function and homology information


acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat ...Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWilliams, A.H. / Dangkulwanich, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM-531310 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM-07184 United States
CitationJournal: Sci Rep / Year: 2019
Title: Structure guided design of an antibacterial peptide that targets UDP-N-acetylglucosamine acyltransferase.
Authors: Dangkulwanich, M. / Raetz, C.R.H. / Williams, A.H.
History
DepositionOct 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
A: TRP-MET-LEU-ASP-PRO-ILE-ALA-GLY-LYS-TRP-SER-ARG


Theoretical massNumber of molelcules
Total (without water)29,5792
Polymers29,5792
Non-polymers00
Water7,206400
1
X: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
A: TRP-MET-LEU-ASP-PRO-ILE-ALA-GLY-LYS-TRP-SER-ARG

X: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
A: TRP-MET-LEU-ASP-PRO-ILE-ALA-GLY-LYS-TRP-SER-ARG

X: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
A: TRP-MET-LEU-ASP-PRO-ILE-ALA-GLY-LYS-TRP-SER-ARG


Theoretical massNumber of molelcules
Total (without water)88,7366
Polymers88,7366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area10360 Å2
ΔGint-69 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.809, 96.809, 96.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11X-575-

HOH

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Components

#1: Protein Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / UDP-N-acetylglucosamine acyltransferase


Mass: 28117.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpxA, b0181, JW0176 / Plasmid: pTO1 / Details (production host): peT23C derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysE
References: UniProt: P0A722, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Protein/peptide TRP-MET-LEU-ASP-PRO-ILE-ALA-GLY-LYS-TRP-SER-ARG


Mass: 1461.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide CR20 / Source: (synth.) Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 51.88 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1.0 M Na/K phosphate, ph 6.3-6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5415 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5415 Å / Relative weight: 1
ReflectionResolution: 1.6→21.65 Å / Num. obs: 34668 / % possible obs: 99.84 % / Redundancy: 3.2 % / Net I/σ(I): 14.2
Reflection shellResolution: 1.6→1.69 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ILxA

Resolution: 1.6→21.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.86 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22639 2011 5 %RANDOM
Rwork0.19694 ---
obs0.19843 37837 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 23.684 Å2
Refinement stepCycle: 1 / Resolution: 1.6→21.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 0 400 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222146
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9382915
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8425284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05823.33393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.82615354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3791516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021634
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.21142
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21483
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4711.51413
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72222203
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2663823
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1034.5706
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.661 133 -
Rwork0.583 2633 -
obs--93.86 %

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