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- PDB-1fmw: CRYSTAL STRUCTURE OF THE MGATP COMPLEX FOR THE MOTOR DOMAIN OF DI... -

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Basic information

Entry
Database: PDB / ID: 1fmw
TitleCRYSTAL STRUCTURE OF THE MGATP COMPLEX FOR THE MOTOR DOMAIN OF DICTYOSTELIUM MYOSIN II
ComponentsMYOSIN II HEAVY CHAINMyosin
KeywordsCONTRACTILE PROTEIN / myosin motor domaim
Function / homologyMyosin, N-terminal, SH3-like / Myosin head (motor domain) / Myosin head, motor domain / Myosin tail / IQ motif, EF-hand binding site / Myosin S1 fragment, N-terminal / Myosin IQ motif-containing domain superfamily / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Myosin tail ...Myosin, N-terminal, SH3-like / Myosin head (motor domain) / Myosin head, motor domain / Myosin tail / IQ motif, EF-hand binding site / Myosin S1 fragment, N-terminal / Myosin IQ motif-containing domain superfamily / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Myosin tail / Myosin N-terminal SH3-like domain / IQ motif profile. / Myosin motor domain profile. / Myosin N-terminal SH3-like domain profile. / uropod retraction / phagocytic cup base / contractile actin filament bundle assembly / response to differentiation-inducing factor 1 / equatorial cell cortex / pseudopodium retraction / cytoplasmic actin-based contraction involved in forward cell motility / cell trailing edge / contractile vacuole organization / myosin filament assembly / actin-myosin filament sliding / culmination involved in sorocarp development / aggregation involved in sorocarp development / hypotonic response / adenyl nucleotide binding / myosin II complex / actomyosin contractile ring / uropod / bleb assembly / detection of mechanical stimulus / filopodium assembly / negative regulation of actin filament polymerization / apical cortex / actin-dependent ATPase activity / myosin filament / microfilament motor activity / early phagosome / actomyosin / 14-3-3 protein binding / cortical actin cytoskeleton / cortical actin cytoskeleton organization / mitotic cytokinesis / cell motility / motor activity / protein localization / response to cAMP / response to mechanical stimulus / extracellular matrix / cell cortex / response to hydrogen peroxide / actin filament binding / chemotaxis / cytoplasmic vesicle / regulation of cell shape / calmodulin binding / cytoskeleton / protein homodimerization activity / ATP binding / identical protein binding / cytosol / Myosin-2 heavy chain
Function and homology information
Specimen sourceDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2.15 Å resolution
AuthorsBauer, C.B. / Holden, H.M. / Thoden, J.B. / Smith, R. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: X-ray structures of the apo and MgATP-bound states of Dictyostelium discoideum myosin motor domain.
Authors: Bauer, C.B. / Holden, H.M. / Thoden, J.B. / Smith, R. / Rayment, I.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 18, 2000 / Release: Nov 22, 2000
RevisionDateData content typeGroupProviderType
1.0Nov 22, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Nov 21, 2012Structure modelAtomic model / Experimental preparation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOSIN II HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2533
Polyers86,7211
Non-polymers5312
Water8,503472
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)104.100, 180.400, 54.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide MYOSIN II HEAVY CHAIN / Myosin


Mass: 86721.086 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN / Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Genus: Dictyostelium / Plasmid name: PBIG / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P08799
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Formula: H2O / Water

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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: 2.93 / Density percent sol: 58.07 %
Crystal growTemp: 277 K / pH: 7.5
Details: 8% Peg 8000, 50 mM Hepes, 1 mM DTT, pH 7.5, microbatch, temperature 277K
Crystal grow
*PLUS
Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
18.0 %(w/v)PEG800011
250 mMHEPES11
31 mMdithiothreitol11
45.0 mg/mlprotein11

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL7-1 / Synchrotron site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Jun 1, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionD resolution high: 2.15 Å / D resolution low: 100 Å / Number all: 54467 / Number obs: 54467 / Rmerge I obs: 0.083 / Redundancy: 2.7 % / Percent possible obs: 96
Reflection
*PLUS
Number measured all: 149338
Reflection shell
*PLUS
Percent possible obs: 95

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Processing

Software
NameVersionClassification
AMoREphasing
TNTrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefineR Free selection details: random / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.286 / R factor R work: 0.206 / R factor all: 0.206 / R factor obs: 0.206 / Highest resolution: 2.15 Å / Lowest resolution: 100 Å / Number reflection R free: 5241 / Number reflection all: 54467 / Number reflection obs: 54467 / Percent reflection obs: 96
Refine hist #LASTHighest resolution: 2.15 Å / Lowest resolution: 100 Å
Number of atoms included #LASTProtein: 5853 / Nucleic acid: 0 / Ligand: 32 / Solvent: 472 / Total: 6357
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.46

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