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- PDB-4wf6: Anthrax toxin lethal factor with bound small molecule inhibitor MK-31 -

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Basic information

Entry
Database: PDB / ID: 4wf6
TitleAnthrax toxin lethal factor with bound small molecule inhibitor MK-31
ComponentsLethal factor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Anthrax toxin / lethal factor / metalloproteinase / metalloprotease / HYDROLASE-HYDROLASE INHIBITOR complex
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 factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / 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 factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / 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-407 / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6521 Å
AuthorsMaize, K.M. / De la Mora-Rey, T. / Finzel, B.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32-GM008700 United States
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
Citation
Journal: J.Med.Chem. / Year: 2015
Title: Probing the S2' Subsite of the Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates.
Authors: Kurbanov, E.K. / Chiu, T.L. / Solberg, J. / Francis, S. / Maize, K.M. / Fernandez, J. / Johnson, R.L. / Hawkinson, J.E. / Walters, M.A. / Finzel, B.C. / Amin, E.A.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: The discovery of a potent and selective lethal factor inhibitor for adjunct therapy of anthrax infection.
Authors: Xiong, Y. / Wiltsie, J. / Woods, A. / Guo, J. / Pivnichny, J.V. / Tang, W. / Bansal, A. / Cummings, R.T. / Cunningham, B.R. / Friedlander, A.M. / Douglas, C.M. / Salowe, S.P. / Zaller, D.M. ...Authors: Xiong, Y. / Wiltsie, J. / Woods, A. / Guo, J. / Pivnichny, J.V. / Tang, W. / Bansal, A. / Cummings, R.T. / Cunningham, B.R. / Friedlander, A.M. / Douglas, C.M. / Salowe, S.P. / Zaller, D.M. / Scolnick, E.M. / Schmatz, D.M. / Bartizal, K. / Hermes, J.D. / MacCoss, M. / Chapman, K.T.
History
DepositionSep 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
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)60,8404
Polymers60,4361
Non-polymers4043
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.400, 75.200, 138.800
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-407 / N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide


Mass: 276.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13FN2O4S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
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: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 17862 / % possible obs: 99 % / Redundancy: 5.4 % / Biso Wilson estimate: 35.01 Å2 / Rmerge(I) obs: 0.106 / Χ2: 0.248 / Net I/av σ(I): 6.962 / Net I/σ(I): 3.8 / Num. measured all: 95814
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.64-2.695.10.4768490.18196.1
2.69-2.735.10.4398580.18897.6
2.73-2.7950.3828380.16796.3
2.79-2.845.10.3628740.18898
2.84-2.9150.38580.16297.6
2.91-2.9750.2738820.20898.7
2.97-3.0550.2438720.17799
3.05-3.1350.2228810.17198.3
3.13-3.2250.1918690.19199.7
3.22-3.3350.1588970.1999.7
3.33-3.445.20.1368770.20399.9
3.44-3.585.30.1019180.206100
3.58-3.755.40.1019040.313100
3.75-3.945.50.088880.226100
3.94-4.195.60.0748950.248100
4.19-4.515.80.0729160.39299.9
4.51-4.975.80.0579160.27399.9
4.97-5.695.90.0659290.257100
5.69-7.166.10.0719430.279100
7.16-506.10.0349980.55598.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQY

1yqy


Resolution: 2.6521→32.487 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 908 5.1 %
Rwork0.1835 16906 -
obs0.1864 17814 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.59 Å2 / Biso mean: 37.5265 Å2 / Biso min: 12.34 Å2
Refinement stepCycle: final / Resolution: 2.6521→32.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 23 112 4228
Biso mean--38.32 33.3 -
Num. residues----503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034187
X-RAY DIFFRACTIONf_angle_d0.6465647
X-RAY DIFFRACTIONf_chiral_restr0.026622
X-RAY DIFFRACTIONf_plane_restr0.003731
X-RAY DIFFRACTIONf_dihedral_angle_d13.291591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6521-2.81820.32911470.24412638278594
2.8182-3.03570.30671620.22942754291698
3.0357-3.34090.2951370.21482798293599
3.3409-3.82370.23841520.172628483000100
3.8237-4.81490.18661670.155528453012100
4.8149-32.48940.2121430.163730233166100

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