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- PDB-1xxe: RDC refined solution structure of the AaLpxC/TU-514 complex -

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Basic information

Entry
Database: PDB / ID: 1xxe
TitleRDC refined solution structure of the AaLpxC/TU-514 complex
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHYDROLASE / LpxC / TU-514 / LPS / lipid A / lipopolysaccharide UDP-3-O-acyl-N-acetylglucosamine deacetylase / metalloamidase / zinc metalloamidase
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TUX / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsCoggins, B.E. / McClerren, A.L. / Jiang, L. / Li, X. / Rudolph, J. / Hindsgaul, O. / Raetz, C.R.H. / Zhou, P.
CitationJournal: Biochemistry / Year: 2005
Title: Refined Solution Structure of the LpxC-TU-514 Complex and pK(a) Analysis of an Active Site Histidine: Insights into the Mechanism and Inhibitor Design
Authors: Coggins, B.E. / McClerren, A.L. / Jiang, L. / Li, X. / Rudolph, J. / Hindsgaul, O. / Raetz, C.R.H. / Zhou, P.
History
DepositionNov 4, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionNov 23, 2004ID: 1NZT
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6913
Polymers32,1941
Non-polymers4972
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / E.C.3.5.1.- / UDP-3-O-acyl-GlcNAc deacetylase


Mass: 32193.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: complexed with TU-514 / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: LpxC / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR
References: UniProt: O67648, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TUX / 1,5-ANHYDRO-2-C-(CARBOXYMETHYL-N-HYDROXYAMIDE)-2-DEOXY-3-O-MYRISTOYL-D-GLUCITOL / TU-514


Mass: 431.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H41NO7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
4143D 15N-separated NOESY
1213D 13C-separated NOESY
3333D 13C-separated NOESY
343RDC
454HNCO-based RDC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM U-15N/13C AaLpxC/TU-51425 mM sodium phosphate, pH 6.5, 100 mM KCl, 2 mM DTT, 5% deuterated-DMSO and 5% D2O
20.5 mM deuterated, 15N/13C, VIL-methyl protonated AaLpxC with TU-51425 mM sodium phosphate, pH 6.5, 100 mM KCl, 2 mM DTT, 5% deuterated-DMSO and 5% D2O
313C-TU514/15N AaLpxC25 mM sodium phosphate, pH 6.5, 100 mM KCl, 2 mM DTT, 5% deuterated-DMSO and 95% D2O
40.5 mM U-15N AaLpxC/TU-51425 mM sodium phosphate, pH 6.5, 100 mM KCl, 2 mM DTT, 5% deuterated-DMSO and 5% D2O
Sample conditionsIonic strength: 100 mM KCl / pH: 6.5 / Pressure: ambient / Temperature: 323 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert P., Mumenthaler C., Wuthrich K.structure solution
XPLOR-NIH2.9.7Schwieters C.D., Kuszewski J.J., Tjandra N., Marius Clore G.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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