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- PDB-4pkw: Anthrax toxin lethal factor with bound small molecule inhibitor GM6001 -

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Basic information

Entry
Database: PDB / ID: 4pkw
TitleAnthrax toxin lethal factor with bound small molecule inhibitor GM6001
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-GM6 / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
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
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 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.number_atoms_total / _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)61,1987
Polymers60,4361
Non-polymers7626
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.427, 82.420, 130.550
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, 392 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GM6 / 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE / GM6001


Mass: 388.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N4O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / 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.: 386 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
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: Jul 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→130.55 Å / Num. obs: 56847 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 26.8 / Num. measured all: 364950

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALAdata scaling
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→41.381 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2878 5.07 %
Rwork0.1772 53891 -
obs0.1787 56769 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.03 Å2 / Biso mean: 27.6386 Å2 / Biso min: 10.6 Å2
Refinement stepCycle: final / Resolution: 1.75→41.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3989 0 73 386 4448
Biso mean--28.4 34.06 -
Num. residues----491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074144
X-RAY DIFFRACTIONf_angle_d1.0565589
X-RAY DIFFRACTIONf_chiral_restr0.043616
X-RAY DIFFRACTIONf_plane_restr0.005719
X-RAY DIFFRACTIONf_dihedral_angle_d14.5331575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.77870.28481030.209725522655
1.7787-1.80940.22771220.211625332655
1.8094-1.84230.26571390.201625492688
1.8423-1.87770.24241410.188725172658
1.8777-1.9160.23341400.177125542694
1.916-1.95770.22991230.17825122635
1.9577-2.00320.19281400.181125522692
2.0032-2.05330.22281440.180725342678
2.0533-2.10880.22211500.183625292679
2.1088-2.17090.23361510.181525212672
2.1709-2.2410.2031600.171325232683
2.241-2.3210.23091470.180625362683
2.321-2.4140.19691370.18425602697
2.414-2.52380.22591210.183725502671
2.5238-2.65690.24411250.188326012726
2.6569-2.82330.22121180.185725782696
2.8233-3.04120.22191270.192426162743
3.0412-3.34710.20371500.182325702720
3.3471-3.83120.20061410.16726022743
3.8312-4.82570.16981480.146126392787
4.8257-41.39210.18341510.179127632914

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