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- PDB-5jxx: Crystal structure of UDP-N-acetylglucosamine O-acyltransferase (L... -

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Basic information

Entry
Database: PDB / ID: 5jxx
TitleCrystal structure of UDP-N-acetylglucosamine O-acyltransferase (LpxA) from Moraxella catarrhalis RH4.
ComponentsAcyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
KeywordsTRANSFERASE / UDP-N-acetylglucosamine O-acyltransferase / LpxA / 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 / 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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...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 / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsPratap, S. / Kesari, P. / Yadav, R. / Narwal, M. / Dev, A. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
ICMR64/3/2012-BMS India
CitationJournal: Int. J. Biol. Macromol. / Year: 2017
Title: Acyl chain preference and inhibitor identification of Moraxella catarrhalis LpxA: Insight through crystal structure and computational studies.
Authors: Pratap, S. / Kesari, P. / Yadav, R. / Dev, A. / Narwal, M. / Kumar, P.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
B: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
C: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
D: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
E: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
F: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,63119
Polymers168,2406
Non-polymers1,39113
Water73941
1
A: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
C: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
E: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7709
Polymers84,1203
Non-polymers6506
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-26 kcal/mol
Surface area30730 Å2
MethodPISA
2
B: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
D: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
F: Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,86210
Polymers84,1203
Non-polymers7427
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-27 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.611, 136.897, 90.585
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28040.043 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (strain BBH18) (bacteria)
Strain: BBH18 / Gene: lpxA, MCR_0549
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D5VAW8, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.05 M Citric Bis-Tris, Propane, pH 5.0, 16% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→45.39 Å / Num. obs: 30503 / % possible obs: 80 % / Redundancy: 2.7 % / Net I/σ(I): 4.76
Reflection shellResolution: 3.001→3.108 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E6U

4e6u


Resolution: 3.001→45.39 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2929 1507 4.95 %
Rwork0.2352 --
obs0.238 30450 78.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.001→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11748 0 92 41 11881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212012
X-RAY DIFFRACTIONf_angle_d0.57816207
X-RAY DIFFRACTIONf_dihedral_angle_d12.7727226
X-RAY DIFFRACTIONf_chiral_restr0.0511845
X-RAY DIFFRACTIONf_plane_restr0.0022115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0006-3.09750.4736320.3429480X-RAY DIFFRACTION14
3.0975-3.20810.3146530.32171023X-RAY DIFFRACTION31
3.2081-3.33650.3204970.32021846X-RAY DIFFRACTION55
3.3365-3.48830.33291380.30352567X-RAY DIFFRACTION77
3.4883-3.67220.34741470.26593015X-RAY DIFFRACTION91
3.6722-3.90210.36211590.25283292X-RAY DIFFRACTION97
3.9021-4.20320.32051740.23513326X-RAY DIFFRACTION99
4.2032-4.62580.24471740.19023316X-RAY DIFFRACTION99
4.6258-5.29430.27821680.20233381X-RAY DIFFRACTION99
5.2943-6.66690.31881910.24593328X-RAY DIFFRACTION100
6.6669-45.3950.21111740.20013369X-RAY DIFFRACTION98

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