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- PDB-2aq9: Structure of E. coli LpxA with a bound peptide that is competitiv... -

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Basic information

Entry
Database: PDB / ID: 2aq9
TitleStructure of E. coli LpxA with a bound peptide that is competitive with acyl-ACP
Components
  • Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
  • peptide inhibitor
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / LpxA / peptide inhibitor / acyl ACP / ACP / UDP-glcNac / Lipid A / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
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
PHOSPHATE ION / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWilliams, A.H. / Immormino, R.M. / Gewirth, D.T. / Raetz, C.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of UDP-N-acetylglucosamine acyltransferase with a bound antibacterial pentadecapeptide.
Authors: Williams, A.H. / Immormino, R.M. / Gewirth, D.T. / Raetz, C.R.
History
DepositionAug 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 42MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,J.M.WORD URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REFERENCE : NEW TOOLS AND DATA FOR IMPROVING : STRUCTURES, USING ALL-ATOM CONTACTS : METHODS IN ENZYMOLOGY. 2003;374:385-412. MOLPROBITY OUTPUT SCORES: ALL-ATOM CLASHSCORE : 6.42 (4.23 B<40) LPXA (PROTEIN CHAIN) BAD ROTAMERS : 0.5% 1/204 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 0.0% 0/260 (TARGET 0.2%) RAMACHANDRAN FAVORED : 97.7% 254/260 (TARGET 98.0%) PEPTIDE 920 (PEPTIDE INHIBITOR OF LPXA) BAD ROTAMERS : 0.0% 0/9 (TARGET 0-1%) RAMACHANDRAN OUTLIERS : 0.0% 0/10 (TARGET 0.2%) RAMACHANDRAN FAVORED :100.0% 10/10 (TARGET 98.0%)
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THERE IS ONE COPY OF THE LPXA MONOMER BOUND TO ONE INHIBITORY PEPTIDE PER ASYMMETRIC UNIT. THE BIOLOGICALLY ACTIVE LPXA MOLECULE, WHICH IS A HOMO-TRIMER, SITS ON A CRYSTALLOGRAPHIC THREE-FOLD AXIS. SWITCHING THE INDEX OF THE LPXA-PEPTIDE COMPLEX FROM THE CUBIC P2(1)3 TO THE ORTHORHOMBIC P2(1)2(1)2(1), WHICH IS THE MAXIMAL NON-ISOMORPHIC SUBGROUP LACKING THE THREE-FOLD AXIS, RESULTS IN A TRIPLING OF MOLECULES IN THE ASYMMETRIC UNIT, AND THE FORMATION OF THE BIOLOGICALLY ACTIVE TRIMER.
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
X: peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,00429
Polymers29,8102
Non-polymers2,19427
Water5,350297
1
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
X: peptide inhibitor
hetero molecules

A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
X: peptide inhibitor
hetero molecules

A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
X: peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,01187
Polymers89,4306
Non-polymers6,58181
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Buried area24900 Å2
ΔGint-34 kcal/mol
Surface area30300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.734, 96.734, 96.734
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
11A-617-

HOH

21A-637-

HOH

31A-639-

HOH

DetailsThe biological unit is a trimer generated by expansion of the monomer around the crystallographic three fold axis

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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) / Strain: K12 / Gene: lpxA / Plasmid: pPET23c-Lpxa(1-262) pT01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysE
References: UniProt: P0A722, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Protein/peptide peptide inhibitor


Mass: 1692.937 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.7 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: DMSO, Sodium Potassium phosphate, pH 6.3-6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 6, 2005 / Details: YALE MIRRORS
RadiationMonochromator: copper Kalpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→18 Å / Num. obs: 28264 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 27.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 25.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 2805 / Rsym value: 0.757 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LXA

1lxa


Resolution: 1.8→18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 354940.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2283 8.6 %RANDOM
Rwork0.194 ---
all-28206 --
obs-26451 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.6868 Å2 / ksol: 0.34244 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 113 297 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.42
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.512.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.321 221 9.2 %
Rwork0.321 2188 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4PO4.paramPO4.top
X-RAY DIFFRACTION5DMSO.paramDMSO.top

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