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- PDB-1jky: Crystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF... -

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Basic information

Entry
Database: PDB / ID: 1jky
TitleCrystal Structure of the Anthrax Lethal Factor (LF): Wild-type LF Complexed with the N-terminal Sequence of MAPKK2
Components
  • Lethal Factor
  • mitogen-activated protein kinase kinase 2
KeywordsTOXIN / Lethal Toxin / Mek2 / MAPKK / Uncleaved substrate / Protease-substrate complex
Function / homology
Function and homology information


anthrax lethal factor endopeptidase / epithelial cell proliferation involved in lung morphogenesis / JUN kinase kinase activity / regulation of axon regeneration / mitogen-activated protein kinase kinase / MAP-kinase scaffold activity / peptidyl-serine autophosphorylation / Signaling by MAP2K mutants / positive regulation of axonogenesis / regulation of Golgi inheritance ...anthrax lethal factor endopeptidase / epithelial cell proliferation involved in lung morphogenesis / JUN kinase kinase activity / regulation of axon regeneration / mitogen-activated protein kinase kinase / MAP-kinase scaffold activity / peptidyl-serine autophosphorylation / Signaling by MAP2K mutants / positive regulation of axonogenesis / regulation of Golgi inheritance / peroxisomal membrane / host cell cytosol / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / positive regulation of cell motility / regulation of stress-activated MAPK cascade / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / MAPK1 (ERK2) activation / face development / MAP kinase kinase activity / Uptake and function of anthrax toxins / thyroid gland development / Schwann cell development / positive regulation of protein serine/threonine kinase activity / myelination / ERK1 and ERK2 cascade / protein serine/threonine/tyrosine kinase activity / insulin-like growth factor receptor signaling pathway / protein serine/threonine kinase activator activity / thymus development / Signal transduction by L1 / PDZ domain binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / metalloendopeptidase activity / cytoplasmic side of plasma membrane / metallopeptidase activity / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / Signaling by BRAF and RAF1 fusions / late endosome / cell-cell junction / heart development / toxin activity / protein tyrosine kinase activity / scaffold protein binding / microtubule / early endosome / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / positive regulation of gene expression / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / mitochondrion / proteolysis / zinc ion binding / extracellular region / ATP binding / metal ion binding / nucleus / cytosol
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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Lethal factor / Dual specificity mitogen-activated protein kinase kinase 2
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 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
DepositionJul 13, 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 8, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND THE AUTHORS NOTE THAT THE MAPKK2 16MER PEPTIDE BOUND IN THE ACTIVE SITE OF THE LETHAL ...COMPOUND THE AUTHORS NOTE THAT THE MAPKK2 16MER PEPTIDE BOUND IN THE ACTIVE SITE OF THE LETHAL FACTOR PROTEIN INFERRED FROM THIS STRUCTURE IS NOT IN THE PRODUCTIVE ORIENTATION FOR PROTEOLYSIS. PLEASE REFER TO THE STRUCTURES WITH PDB ID CODES 1PWV AND 1PWW, FOR THE PRODUCTIVE CONFORMATION OF AN OPTIMAL PEPTIDE SUBSTRATE BOUND IN THE LETHAL FACTOR ACTIVE SITE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lethal Factor
B: mitogen-activated protein kinase kinase 2


Theoretical massNumber of molelcules
Total (without water)92,1502
Polymers92,1502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)330.700, 330.700, 330.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Lethal Factor / LF


Mass: 90356.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MATURE FORM / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): BH441 / References: UniProt: P15917
#2: Protein/peptide mitogen-activated protein kinase kinase 2 / MAPKK2 / Mek2


Mass: 1793.247 Da / Num. of mol.: 1 / Fragment: N-terminus / Source method: obtained synthetically
Details: This protein was chemically synthesized. It is based on a sequence from Homo sapiens (human).
References: GenBank: 13489054, UniProt: P36507*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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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: 8.4 Å3/Da / Density % sol: 86 %
Crystal growpH: 8 / Details: 1.9M Ammonium sulfate, 0.2M Tris pH 8.0, 2mM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 2001
RadiationMonochromator: 0.87 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.9→50.6 Å / Num. all: 22906 / Num. obs: 22906 / % possible obs: 84.9 % / Redundancy: 3.7 % / Rsym value: 0.103 / Net I/σ(I): 12.9
Reflection shellResolution: 3.9→4 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.631 / % possible all: 88.1

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Processing

Software
NameVersionClassification
DENZODENZOdata reduction
SCALEPACKDENZOdata scaling
CCP4MOLREPmodel building
REFMACrefinement
CNSrefinement
CCP4(MOLREP)phasing
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J7N

1j7n


Resolution: 3.9→50.6 Å / Cor.coef. Fo:Fc: 0.886 / SU B: 27.142 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.6 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1154 4.8 %RANDOM
Rwork0.296 ---
obs0.296 22906 85 %-
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 118.741 Å2
Refinement stepCycle: LAST / Resolution: 3.9→50.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5734 0 0 0 5734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_chiral_restr0.114
X-RAY DIFFRACTIONp_xyhbond_nbd0.307
X-RAY DIFFRACTIONp_mcbond_it1.415
X-RAY DIFFRACTIONp_mcangle_it2.417
X-RAY DIFFRACTIONp_scbond_it1.245
X-RAY DIFFRACTIONp_scangle_it2.072
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.403 84
Rwork0.387 1741

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