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- PDB-2xel: Molecular Mechanism of Pentachloropseudilin Mediated Inhibition o... -

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Basic information

Entry
Database: PDB / ID: 2xel
TitleMolecular Mechanism of Pentachloropseudilin Mediated Inhibition of Myosin Motor Activity
ComponentsMYOSIN-2 HEAVY CHAIN
KeywordsMOTOR PROTEIN / CONTRACTILE PROTEIN / ALLOSTERIC INHIBITOR / NON-HYDROYLSABLE ATP ANALOGUE
Function / homology
Function and homology information


calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / RHO GTPases activate PAKs / contractile actin filament bundle assembly ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / RHO GTPases activate PAKs / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / adenyl nucleotide binding / actomyosin contractile ring / hypotonic response / uropod / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / myosin filament / filopodium assembly / myosin II complex / early phagosome / microfilament motor activity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / response to mechanical stimulus / response to cAMP / extracellular matrix / 14-3-3 protein binding / cell motility / response to hydrogen peroxide / protein localization / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. ...Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADP METAVANADATE / Chem-IA2 / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChinthalapudi, K. / Taft, M.H. / Martin, R. / Hartmann, F.K. / Heissler, S.M. / Tsiavaliaris, G. / Gutzeit, H.O. / Knoelker, H.J. / Coluccio, L.M. / Fedorov, R. / Manstein, D.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Mechanism and Specificity of Pentachloropseudilin-Mediated Inhibition of Myosin Motor Activity.
Authors: Chinthalapudi, K. / Taft, M.H. / Martin, R. / Heissler, S.M. / Preller, M. / Hartmann, F.K. / Brandstaetter, H. / Kendrick-Jones, J. / Tsiavaliaris, G. / Gutzeit, H.O. / Fedorov, R. / Buss, ...Authors: Chinthalapudi, K. / Taft, M.H. / Martin, R. / Heissler, S.M. / Preller, M. / Hartmann, F.K. / Brandstaetter, H. / Kendrick-Jones, J. / Tsiavaliaris, G. / Gutzeit, H.O. / Fedorov, R. / Buss, F. / Knoelker, H.J. / Coluccio, L.M. / Manstein, D.J.
History
DepositionMay 16, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOSIN-2 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3974
Polymers88,5141
Non-polymers8833
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.530, 147.490, 153.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MYOSIN-2 HEAVY CHAIN / / MYOSIN II HEAVY CHAIN


Mass: 88513.969 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESUDES 2-761
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Plasmid: PDXA-3H / Production host: DICTYOSTELIUM DISCOIDEUM (eukaryote) / References: UniProt: P08799
#2: Chemical ChemComp-AD9 / ADP METAVANADATE


Mass: 527.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P2V
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-IA2 / 2,4-DICHLORO-6-(3,4,5-TRICHLORO-1H-PYRROL-2YL)PHENOL


Mass: 331.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H4Cl5NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsADP-METAVANADATE: NON-HYDROLYSABLE ATP ANALOGUE. PENTACHLOROPSEUDILIN: 2,4-DICHLORO-6-(3,4,5- ...ADP-METAVANADATE: NON-HYDROLYSABLE ATP ANALOGUE. PENTACHLOROPSEUDILIN: 2,4-DICHLORO-6-(3,4,5-TRICHLORO-1H-PYRROL-2- YL)PHENOL
Sequence detailsMOTOR DOMAIN(2-761)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.56 % / Description: NONE
Crystal growDetails: 50 MM HEPES PH 7.4, 140 MM NACL, 11% W/V PEG8000, 2% (V/V) MPD, 5 MM MGCL2, 5 MM DTT, 1 MM EGTA.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: RAYONIX / Detector: CCD / Date: Jul 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 35588 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.97
Reflection shellResolution: 2.5→2.8 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 6.99 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→24.59 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: BULK SOLVENT MODEL USED RESIDUES 698 TO 777 ARE DISORDERED REGION. THEY WERE MODELED STEREOCHEMICALLY BASED ON THE STRUCTURE 2JHR
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1777 5 %RANDOM
Rwork0.229 ---
obs0.229 35532 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.6845 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 53.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.93 Å20 Å20 Å2
2--5.03 Å20 Å2
3----11.96 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6239 0 49 458 6746
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.7
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_d1.58
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ADPVO3.PARADPVO3.TOP
X-RAY DIFFRACTION5IA2.PARIA2.TOP

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