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- PDB-4pkr: Anthrax toxin lethal factor with bound small molecule inhibitor 10 -

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Basic information

Entry
Database: PDB / ID: 4pkr
TitleAnthrax toxin lethal factor with bound small molecule inhibitor 10
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-2ZL / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 Allergy and Infectious Diseases (NIH/NIAID)AI091790-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM08700 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.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

Downloads & links

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Assembly

Deposited unit
A: Lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9955
Polymers60,4361
Non-polymers5594
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.200, 78.000, 134.700
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, 312 molecules

#2: Chemical ChemComp-2ZL / N~2~-benzyl-N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-D-alaninamide


Mass: 366.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19FN2O4S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
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: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→44.89 Å / Num. obs: 27371 / % possible obs: 95.4 % / Redundancy: 6.62 % / Biso Wilson estimate: 23.91 Å2 / Rmerge(I) obs: 0.143 / Χ2: 1.12 / Net I/σ(I): 8.7 / Num. measured all: 182509 / Scaling rejects: 1369
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.2-2.286.780.5272.91766125851.5612991.5
2.28-2.376.810.4293.71765825831.237191.1
2.37-2.486.770.3854.21760725891.227192.2
2.48-2.616.680.3374.71776726491.27292.9
2.61-2.776.60.2865.51772326721.179094.9
2.77-2.996.590.2196.91793427061.111095.2
2.99-3.296.430.1688.71810327951.0413197.3
3.29-3.766.380.13911.21830428161.0332698
3.76-4.746.520.07717.41923929150.8422199.9
4.74-44.896.650.07119.52051330610.91148100

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Processing

Software
NameVersionClassification
d*TREK9.9.9.5Ldata reduction
PDB_EXTRACT3.14data extraction
PHENIX1.8.4_1496refinement
RefinementResolution: 2.2→39 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1377 5.05 %
Rwork0.2042 25914 -
obs0.2067 27291 95.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.52 Å2 / Biso mean: 30.4009 Å2 / Biso min: 13.05 Å2
Refinement stepCycle: final / Resolution: 2.2→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 33 308 4417
Biso mean--32.59 31.13 -
Num. residues----495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024185
X-RAY DIFFRACTIONf_angle_d0.6455638
X-RAY DIFFRACTIONf_chiral_restr0.025615
X-RAY DIFFRACTIONf_plane_restr0.003729
X-RAY DIFFRACTIONf_dihedral_angle_d14.1621609
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.27790.41521290.38212400252989
2.2779-2.36910.34361360.25962449258591
2.3691-2.47690.27461150.23642473258892
2.4769-2.60740.32341330.22632516264993
2.6074-2.77080.2871330.22612542267595
2.7708-2.98460.26161310.2222572270395
2.9846-3.28480.29141510.21992645279697
3.2848-3.75980.26241500.19292669281998
3.7598-4.73570.19011430.148227652908100
4.7357-39.00610.18031560.168728833039100

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