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- PDB-4xm6: Anthrax toxin lethal factor with ligand-induced binding pocket -

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Basic information

Entry
Database: PDB / ID: 4xm6
TitleAnthrax toxin lethal factor with ligand-induced binding pocket
ComponentsLethal factor
KeywordsTOXIN / HYDROLASE / Anthrax toxin / lethal factor / metalloproteinase / metalloprotease / structural dynamics / ligand-induced conformational change
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, domain 3, chain A / Anthrax toxin lethal factor, domain 3, chain A / Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Anthrax toxin, lethal/endema factor / Anthrax toxin, lethal/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like domain profile. / Toxin ADP-ribosyltransferase; Chain A, domain 1 ...Anthrax toxin lethal factor, domain 3, chain A / Anthrax toxin lethal factor, domain 3, chain A / Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Anthrax toxin, lethal/endema factor / Anthrax toxin, lethal/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like domain profile. / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-41R / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.352 Å
AuthorsMaize, K.M. / De la Mora-Rey, T. / Finzel, B.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI091790-01 United States
Minnesota Dept. of Employment and Economic DevelopmentSPAP-06-0014-P-FY07 United States
CitationJournal: Febs Lett. / Year: 2015
Title: Ligand-induced expansion of the S1' site in the anthrax toxin lethal factor.
Authors: Maize, K.M. / Kurbanov, E.K. / Johnson, R.L. / Amin, E.A. / Finzel, B.C.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9865
Polymers60,4361
Non-polymers5504
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.936, 76.922, 138.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 60436.047 Da / Num. of mol.: 1 / Fragment: UNP residues 298-809 / Mutation: A266S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: lef, pXO1-107, BXA0172, GBAA_pXO1_0172 / Plasmid: pMCSG10 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS
References: UniProt: P15917, anthrax lethal factor endopeptidase
#2: Chemical ChemComp-41R / N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-N~2~-(2-methylpropyl)-D-valinamide


Mass: 360.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25FN2O4S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 11-16% PEG 8K, 50 mM Bis-Tris, 100 mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 25999 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 40.49 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.054 / Net I/av σ(I): 25.473 / Net I/σ(I): 12.3 / Num. measured all: 93815
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.392.90.24710700.75883.2
2.39-2.433.40.25612390.75995.4
2.43-2.483.50.22412910.75397.3
2.48-2.533.50.2212800.77397.5
2.53-2.593.60.17712550.75297
2.59-2.653.50.16112800.896.8
2.65-2.713.60.1612460.90597
2.71-2.793.50.13913080.90797.5
2.79-2.873.60.11912800.92597.9
2.87-2.963.60.10213130.96999.2
2.96-3.073.70.08513130.9699.5
3.07-3.193.70.07513071.01299.5
3.19-3.333.80.0613231.03799.8
3.33-3.513.80.05113311.2100
3.51-3.733.80.04613271.487100
3.73-4.023.80.04213471.38699.9
4.02-4.423.80.03913461.55299.9
4.42-5.063.70.03413591.3199.9
5.06-6.373.70.03413841.0799.6
6.37-503.60.03214001.35895

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQY

1yqy


Resolution: 2.352→23.38 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 1316 5.08 %
Rwork0.205 24601 -
obs0.2071 25917 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.95 Å2 / Biso mean: 49.2515 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.352→23.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3995 0 33 121 4149
Biso mean--52.16 41.95 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054095
X-RAY DIFFRACTIONf_angle_d0.8895512
X-RAY DIFFRACTIONf_chiral_restr0.036604
X-RAY DIFFRACTIONf_plane_restr0.003710
X-RAY DIFFRACTIONf_dihedral_angle_d14.7441573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.352-2.44610.27391200.2492590271094
2.4461-2.55730.33441350.24982680281597
2.5573-2.69190.32261510.25822644279597
2.6919-2.86030.2791410.25152678281998
2.8603-3.08070.27841340.26342755288999
3.0807-3.38990.28241590.230627582917100
3.3899-3.87850.24441470.191227992946100
3.8785-4.87920.1991610.16592794295599
4.8792-23.38140.21541680.17832903307199

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