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- PDB-4pks: Anthrax toxin lethal factor with bound small molecule inhibitor 11 -

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Basic information

Entry
Database: PDB / ID: 4pks
TitleAnthrax toxin lethal factor with bound small molecule inhibitor 11
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 / extracellular region / zinc ion binding
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-30H / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsMaize, K.M. / De la Mora, T. / Finzel, B.C.
Funding support United States, 3items
OrganizationGrant numberCountry
Minnesota Dept. of Employment and Economic DevelopmentSPAP-06-0014-P-FY07 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM08700 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI091790-01 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Anthrax toxin lethal factor domain 3 is highly mobile and responsive to ligand binding.
Authors: Maize, K.M. / Kurbanov, E.K. / De La Mora-Rey, T. / Geders, T.W. / Hwang, D.J. / Walters, M.A. / Johnson, R.L. / Amin, E.A. / Finzel, B.C.
History
DepositionMay 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Derived calculations
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0856
Polymers60,4361
Non-polymers6495
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 77.890, 134.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 225 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-30H / N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-N~2~-(pyridin-3-ylmethyl)-D-alaninamide


Mass: 367.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18FN3O4S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
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: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.92 Å / Num. obs: 25017 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 30.87 Å2 / Rmerge(I) obs: 0.159 / Χ2: 1.08 / Net I/σ(I): 7.1 / Num. measured all: 173958 / Scaling rejects: 1305
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.3-2.386.870.5152.81687824560.99199.6
2.38-2.486.860.47731689424620.990100
2.48-2.596.870.4643.21712824911.086100
2.59-2.736.970.3943.71701624421.083100
2.73-2.96.980.3254.61738024841.1438100
2.9-3.127.040.2595.61759424891.1476100
3.12-3.4470.2067.11759624881.22170100
3.44-3.936.930.1519.41766525021.2733199.8
3.93-4.956.870.0914.41775925260.9939599.4
4.95-44.926.640.07116.81804826770.8628599.9

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Processing

Software
NameVersionClassification
d*TREK9.9.9.5Ldata reduction
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.3→38.945 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 1271 5.09 %
Rwork0.209 23695 -
obs0.2117 24966 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.57 Å2 / Biso mean: 35.5631 Å2 / Biso min: 14.81 Å2
Refinement stepCycle: final / Resolution: 2.3→38.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 40 220 4265
Biso mean--37.29 35.65 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044114
X-RAY DIFFRACTIONf_angle_d0.7255537
X-RAY DIFFRACTIONf_chiral_restr0.027603
X-RAY DIFFRACTIONf_plane_restr0.004714
X-RAY DIFFRACTIONf_dihedral_angle_d15.4611578
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 (%)
2.3-2.3920.30671420.23525772719100
2.392-2.50090.34121530.240225972750100
2.5009-2.63270.28581250.24425992724100
2.6327-2.79760.33931400.243325852725100
2.7976-3.01350.27421480.233126242772100
3.0135-3.31660.3131490.233426162765100
3.3166-3.79620.26021180.208926642782100
3.7962-4.78150.21161540.17492642279699
4.7815-38.95060.2081420.18222791293399

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