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- PDB-2l0r: Conformational Dynamics of the Anthrax Lethal Factor Catalytic Center -

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Basic information

Entry
Database: PDB / ID: 2l0r
TitleConformational Dynamics of the Anthrax Lethal Factor Catalytic Center
ComponentsLethal factor
KeywordsHYDROLASE / TOXIN / protein / Anthrax Lethal Factor / catalytic domain / Zn metalloprotease / Bacillus Anthracis
Function / homology
Function and homology information


anthrax lethal factor endopeptidase / host cell cytosol / Uptake and function of anthrax toxins / metalloendopeptidase activity / metallopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily ...Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodSOLUTION NMR / Molexular mechanics
Model detailsminimized average, model 1
AuthorsDalkas, G.A. / Chasapis, C.T. / Gkazonis, P.V. / Bentrop, D.A. / Spyroulias, G.A.
CitationJournal: Biochemistry / Year: 2010
Title: Conformational dynamics of the anthrax lethal factor catalytic center.
Authors: Dalkas, G.A. / Chasapis, C.T. / Gkazonis, P.V. / Bentrop, D. / Spyroulias, G.A.
History
DepositionJul 15, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lethal factor


Theoretical massNumber of molelcules
Total (without water)12,1391
Polymers12,1391
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / 31target function
RepresentativeModel #1minimized average

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Components

#1: Protein Lethal factor / LF / Anthrax lethal toxin endopeptidase component


Mass: 12139.410 Da / Num. of mol.: 1
Fragment: C-terminal 106 residues catalytic core domain (Domain IV), UNP residues 705-809
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BXA0172, GBAA_pXO1_0172, lef, pXO1-107 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P15917, anthrax lethal factor endopeptidase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D HNHA
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1912D (HB)CB(CGCD)HDarom
11012D 2J-edited 1H-15N HSQC

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Sample preparation

DetailsContents: 0.6 mM [U-99% 13C; U-99% 15N] Anthrax LF C-term-1, 10 % % [U-99% 2H] D2O-2, 90 % % H2O-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMAnthrax LF C-term-1[U-99% 13C; U-99% 15N]1
10 %D2O-2[U-99% 2H]1
90 %H2O-31
Sample conditionsIonic strength: Pi 50 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE4002

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Processing

NMR software
NameVersionDeveloperClassification
DYANAGuntert, Braun and Wuthrichstructure solution
Amber5Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: Molexular mechanics / Software ordinal: 1
Details: Energy minimization, bond lengths/angles optimization
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 31 / Conformers submitted total number: 31

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