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- PDB-5d1s: Anthrax toxin lethal factor with hydroxamic acid inhibitor -

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Basic information

Entry
Database: PDB / ID: 5d1s
TitleAnthrax toxin lethal factor with hydroxamic acid inhibitor
ComponentsLethal factor
KeywordsHydrolase/hydrolase inhibitor / Anthrax toxin / lethal factor / metalloproteinase / metalloprotease / structural dynamics / ligand-induced conformational change / 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-56Q / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMaize, K.M. / Finzel, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI091790-01 United States
CitationJournal: 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.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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)60,7923
Polymers60,4361
Non-polymers3562
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.780, 78.277, 138.209
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: residues 298-809 / Mutation: A299S
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-56Q / N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-N~2~-methyl-D-alaninamide


Mass: 290.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15FN2O4S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→138.209 Å / Num. obs: 37424 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.01 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.1 / Num. measured all: 242868
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique all
2.1-2.1076.50.3732584395
9.746-138.2095.80.0272556442

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
PHENIXrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQY

1yqy


Resolution: 2.1→39.704 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 1812 4.85 %
Rwork0.2014 35534 -
obs0.2036 37346 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.79 Å2 / Biso mean: 37.5872 Å2 / Biso min: 11.78 Å2
Refinement stepCycle: final / Resolution: 2.1→39.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4037 0 20 166 4223
Biso mean--38.45 34.52 -
Num. residues----507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084128
X-RAY DIFFRACTIONf_angle_d1.0545585
X-RAY DIFFRACTIONf_chiral_restr0.039625
X-RAY DIFFRACTIONf_plane_restr0.005725
X-RAY DIFFRACTIONf_dihedral_angle_d14.5941529
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15680.35281430.262826972840100
2.1568-2.22030.32691210.24627192840100
2.2203-2.29190.28891250.23226862811100
2.2919-2.37380.30391480.233427052853100
2.3738-2.46880.2681250.229426932818100
2.4688-2.58120.33541240.231327172841100
2.5812-2.71720.28551380.22827312869100
2.7172-2.88740.23971320.23227302862100
2.8874-3.11030.30631440.233326992843100
3.1103-3.42320.27591740.228627022876100
3.4232-3.91810.23171450.184527682913100
3.9181-4.93490.19711450.16127742919100
4.9349-39.71070.17711480.15952913306199

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