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- PDB-1pwq: Crystal structure of Anthrax Lethal Factor complexed with Thioace... -

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Basic information

Entry
Database: PDB / ID: 1pwq
TitleCrystal structure of Anthrax Lethal Factor complexed with Thioacetyl-Tyr-Pro-Met-Amide, a metal-chelating peptidyl small molecule inhibitor
ComponentsLethal factor
KeywordsHYDROLASE / Anthrax Toxin / Lethal Factor / metal-chelator / small molecule peptidic inhibitor
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
N-(SULFANYLACETYL)TYROSYLPROLYLMETHIONINAMIDE / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsWong, T.Y. / Schwarzenbacher, R. / Liddington, R.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor.
Authors: Turk, B.E. / Wong, T.Y. / Schwarzenbacher, R. / Jarrell, E.T. / Leppla, S.H. / Collier, R.J. / Liddington, R.C. / Cantley, L.C.
History
DepositionJul 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)181,8106
Polymers180,7142
Non-polymers1,0964
Water00
1
A: Lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9053
Polymers90,3571
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9053
Polymers90,3571
Non-polymers5482
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.700, 137.400, 98.300
Angle α, β, γ (deg.)90.00, 98.00, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: LEF / Plasmid: pX01 / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): BH441
References: UniProt: P15917, 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-SD2 / N-(SULFANYLACETYL)TYROSYLPROLYLMETHIONINAMIDE


Type: L-peptide linking / Mass: 482.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N4O5S2

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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: 3.81 Å3/Da / Density % sol: 67.47 %
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
Crystal grow
*PLUS
Temperature: 21-29 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 Mammonium sulfate1reservoir
20.2 MTris-HCl1reservoirpH8.0
32 mMEDTA1reservoir
413 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.52→30 Å / Num. obs: 28731 / % possible obs: 90.8 % / Observed criterion σ(I): 2 / Rsym value: 0.159 / Net I/σ(I): 7.4
Reflection shellResolution: 3.52→3.6 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.451 / % possible all: 84.9
Reflection
*PLUS
Highest resolution: 3.5 Å / Num. measured all: 91831 / Rmerge(I) obs: 0.159
Reflection shell
*PLUS
% possible obs: 84.9 % / Rmerge(I) obs: 0.451

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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: 3.52→24.86 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 194801.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.311 1331 4.9 %RANDOM
Rwork0.228 ---
obs0.228 27151 86.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.260498 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 3.52→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12054 0 66 0 12120
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it1.512
X-RAY DIFFRACTIONc_scangle_it2.52.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.52→3.66 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.362 108 4.1 %
Rwork0.253 2496 -
obs--65 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3THIOYPM1-1.PARTHIOYPM1-1_SD2.TOP
Software
*PLUS
Version: 1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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