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- PDB-1j7n: Anthrax Toxin Lethal factor -

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Basic information

Entry
Database: PDB / ID: 1j7n
TitleAnthrax Toxin Lethal factor
ComponentsLethal Factor precursor
KeywordsTOXIN / Anthrax / Lethal Toxin / Lethal Factor / Zinc Metalloprotease / MAPKK / MEK
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 / zinc ion binding / extracellular region
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 factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / 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 factor (ATLF)-like domain profile. / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsPannifer, A.D. / Wong, T.Y. / Schwarzenbacher, R. / Renatus, M. / Petosa, C. / Collier, R.J. / Bienkowska, J. / Lacy, D.B. / Park, S. / Leppla, S.H. ...Pannifer, A.D. / Wong, T.Y. / Schwarzenbacher, R. / Renatus, M. / Petosa, C. / Collier, R.J. / Bienkowska, J. / Lacy, D.B. / Park, S. / Leppla, S.H. / Hanna, P. / Liddington, R.C.
CitationJournal: Nature / Year: 2001
Title: Crystal structure of the anthrax lethal factor.
Authors: Pannifer, A.D. / Wong, T.Y. / Schwarzenbacher, R. / Renatus, M. / Petosa, C. / Bienkowska, J. / Lacy, D.B. / Collier, R.J. / Park, S. / Leppla, S.H. / Hanna, P. / Liddington, R.C.
History
DepositionMay 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_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_asym_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_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_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

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Assembly

Deposited unit
A: Lethal Factor precursor
B: Lethal Factor precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,0376
Polymers180,7142
Non-polymers3234
Water16,826934
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-126 kcal/mol
Surface area68060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.201, 137.461, 98.547
Angle α, β, γ (deg.)90.00, 98.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lethal Factor precursor / Anthrax Toxin Lethal Factor


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: pSJ115 / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): BH441 / References: UniProt: P15917
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 934 / 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: 3.6 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate, TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSRS PX9.611.542
SYNCHROTRONESRF BM1420.9502
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999
RadiationMonochromator: Hg- edge / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.5421
20.95021
ReflectionResolution: 2.2→15 Å / Num. all: 523147 / Num. obs: 114503 / % possible obs: 89.5 % / Redundancy: 3.6 % / Rsym value: 0.052 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.137 / % possible all: 89.5

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→15 Å / Cross valid method: R free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS default
RfactorNum. reflection% reflectionSelection details
Rfree0.261 5433 5 %random
Rwork0.2292 ---
all-111935 --
obs-102086 5 %-
Displacement parametersBiso mean: 59.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11978 0 12 934 12924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.41
X-RAY DIFFRACTIONc_mcangle_it2.108
X-RAY DIFFRACTIONc_scbond_it2.03
X-RAY DIFFRACTIONc_scangle_it3
X-RAY DIFFRACTIONc_bond_d0.006092
X-RAY DIFFRACTIONc_angle_deg1.17

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