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- PDB-1lxa: UDP N-ACETYLGLUCOSAMINE ACYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1lxa
TitleUDP N-ACETYLGLUCOSAMINE ACYLTRANSFERASE
ComponentsUDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
KeywordsACYLTRANSFERASE / TRANSFERASE / LIPID A BIOSYNTHESIS / LIPID SYNTHESIS
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 / cytoplasm / cytosol
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
Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsRoderick, S.L.
Citation
Journal: Science / Year: 1995
Title: A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase.
Authors: Raetz, C.R. / Roderick, S.L.
#1: Journal: Proteins / Year: 1995
Title: Crystallization of Udp N-Acetylglucosamine O-Acyltransferase from Escherichia Coli
Authors: Pfitzner, U. / Raetz, C.R.H. / Roderick, S.L.
History
DepositionOct 7, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)28,1171
Polymers28,1171
Non-polymers00
Water00
1
A: UDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE

A: UDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE

A: UDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)84,3513
Polymers84,3513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5150 Å2
ΔGint-39 kcal/mol
Surface area30440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.000, 99.000, 99.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein UDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE / LPXA


Mass: 28117.018 Da / Num. of mol.: 1 / Mutation: S64Q, V65F, D125H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: LPXA / Plasmid: PSR1 / Gene (production host): LPXA / Production host: Escherichia coli (E. coli)
References: UniProt: P0A722, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
Compound detailsMET 1 THROUGH ILE 186 COMPRISES THE LEFT-HANDED BETA-HELICAL DOMAIN WITH TWO LOOP EXCURSIONS.

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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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6.8 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.9 Msodium phosphate1reservoiror potassium phosphate
215-20 %(v/v)dimethylsulfoxide1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. obs: 8868 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Num. measured all: 79727 / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
X-PLORmodel building
TNT5Erefinement
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 2.6→99 Å / Isotropic thermal model: KNOWLEDGE-BASED / σ(F): 0 / Stereochemistry target values: TNT SUPPLIED
RfactorNum. reflection% reflection
Rwork0.184 --
obs-8868 87 %
Solvent computationSolvent model: TWO PARAMETER RECIPROCAL SPACE / Bsol: 250 Å2 / ksol: 0.874 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 0 0 1974
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONx_bond_d0.01220100.8
X-RAY DIFFRACTIONx_angle_deg2.427131.3
X-RAY DIFFRACTIONx_dihedral_angle_d26.412130
Software
*PLUS
Name: X-PLOR/TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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