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- PDB-1zxv: X-Ray Crystal Structure of the Anthrax Lethal Factor Bound to a S... -

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Basic information

Entry
Database: PDB / ID: 1zxv
TitleX-Ray Crystal Structure of the Anthrax Lethal Factor Bound to a Small Molecule Inhibitor, BI-MFM3, 3-{5-[5-(4-Chloro-phenyl)-furan-2-ylmethylene]-4-oxo-2-thioxo-thiazolidin-3-yl}-propionic acid.
Componentslethal factor
KeywordsHYDROLASE / Anthrax Toxin Lethal Factor / protein and small molecule inhibitor complex / zinc metalloproteinase
Function / homology
Function and homology information


: / metallopeptidase activity / extracellular region / metal 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 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Collagenase (Catalytic Domain) ...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 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MFM / : / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsWong, T.Y. / Liddington, R.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Efficient synthetic inhibitors of anthrax lethal factor.
Authors: Forino, M. / Johnson, S. / Wong, T.Y. / Rozanov, D.V. / Savinov, A.Y. / Li, W. / Fattorusso, R. / Becattini, B. / Orry, A.J. / Jung, D. / Abagyan, R.A. / Smith, J.W. / Alibek, K. / ...Authors: Forino, M. / Johnson, S. / Wong, T.Y. / Rozanov, D.V. / Savinov, A.Y. / Li, W. / Fattorusso, R. / Becattini, B. / Orry, A.J. / Jung, D. / Abagyan, R.A. / Smith, J.W. / Alibek, K. / Liddington, R.C. / Strongin, A.Y. / Pellecchia, M.
History
DepositionJun 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lethal factor
B: lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,6326
Polymers180,7142
Non-polymers9194
Water0
1
A: lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8163
Polymers90,3571
Non-polymers4592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8163
Polymers90,3571
Non-polymers4592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.960, 136.650, 97.900
Angle α, β, γ (deg.)90.00, 98.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein lethal factor / LF / Anthrax lethal toxin endopeptidase component


Mass: 90356.812 Da / Num. of mol.: 2 / Fragment: Mature peptide
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: lef / Plasmid: pSJ119 / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): BH441
References: GenBank: 143144, UniProt: Q52NH3*PLUS, anthrax lethal factor endopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MFM / (E)-3-(5((5-(4-CHLOROPHENYL)FURAN-2-YL)METHYLENE)-4-OXO-2-THIOXOTHIAZOLIDIN-3-YL)PROPANOIC ACID


Mass: 393.864 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H12ClNO4S2
Details: Chemically synthesised compound based upon initial virtual ligand screening and protein crystal data of initial leads.

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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: 3.51 Å3/Da / Density % sol: 64.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate, Tris-HCl, EDTA., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 22, 2004 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.67→49 Å / Num. all: 160988 / Num. obs: 70243 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Rsym value: 0.074 / Net I/σ(I): 13.29
Reflection shellResolution: 2.67→2.77 Å / Mean I/σ(I) obs: 1.76 / Num. unique all: 70243 / Rsym value: 0.5945 / % possible all: 99.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J7N

1j7n


Resolution: 2.67→49 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.5
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3306 -Random
Rwork0.231 ---
all-70918 --
obs-65310 98.9 %-
Refinement stepCycle: LAST / Resolution: 2.67→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12036 0 52 0 12088

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