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- PDB-2x9h: CRYSTAL STRUCTURE OF MYOSIN-2 MOTOR DOMAIN IN COMPLEX WITH ADP- M... -

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Basic information

Entry
Database: PDB / ID: 2x9h
TitleCRYSTAL STRUCTURE OF MYOSIN-2 MOTOR DOMAIN IN COMPLEX WITH ADP- METAVANADATE AND PENTACHLOROCARBAZOLE
ComponentsMYOSIN-2 HEAVY CHAIN
KeywordsCONTRACTILE PROTEIN / NUCLEOTIDE-BINDING / MOTOR PROTEIN / ACTIN-BINDING
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 / contractile actin filament bundle assembly / cell trailing edge ...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 / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / adenyl nucleotide binding / actomyosin contractile ring / hypotonic response / uropod / actin-myosin filament sliding / detection of mechanical stimulus / negative regulation of actin filament polymerization / apical cortex / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / myosin II complex / cortical actin cytoskeleton organization / microfilament motor activity / cortical actin cytoskeleton / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / cell motility / response to hydrogen peroxide / chemotaxis / actin filament binding / protein localization / regulation of cell shape / cell cortex / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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. / Kinesin motor domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 type barrels. / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADP METAVANADATE / 2,3,4,6,8-PENTACHLORO-9H-CARBAZOL-1-OL / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSelvadurai, J. / Kirst, J. / Knoelker, H.J. / Manstein, D.J.
Citation
Journal: To be Published
Title: Crystal Structure of Myosin-2 Motor Domain in Complex with Adp-Metavanadate and Pentachlorocarbazole
Authors: Fedrov, R. / Boehl, M. / Tsiavaliaris, G. / Hartmann, F.K. / Baruch, P. / Brenner, B. / Martin, R. / Knoelker, H.J. / Gutzeit, H.O. / Manstein, D.J.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2009
Title: The Mechanism of Pentabromopseudilin Inhibition of Myosin Motor Activity.
Authors: Fedorov, R. / Bohl, M. / Tsiavaliaris, G. / Hartmann, F.K. / Taft, M.H. / Baruch, P. / Brenner, B. / Martin, R. / Knolker, H. / Gutzeit, H.O. / Manstein, D.J.
History
DepositionMar 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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: MYOSIN-2 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8484
Polymers78,9411
Non-polymers9073
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.160, 146.630, 153.680
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 / MYOSIN II HEAVY CHAIN


Mass: 78941.242 Da / Num. of mol.: 1 / Fragment: MYOSIN MOTOR DOMAIN, RESIDUES 2-696
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX3 / Production host: DICTYOSTELIUM DISCOIDEUM (eukaryote) / References: UniProt: P08799, EC: 3.6.4.1
#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-KI9 / 2,3,4,6,8-PENTACHLORO-9H-CARBAZOL-1-OL


Mass: 355.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H4Cl5NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsADP METAVANADATE (AMV): NON-HYDROLYSABLE ATP-ANALOG ADP-METAVANADATE

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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: 3.21 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7.4
Details: 50 MM TRIS-HCL PH 7.4, 140 MM NACL, 9% W/V PEG8000, 2% (V/V) MPD, 5 MM MGCL2, 5 MM DTT, 1 MM EGTA

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 24, 2010
Details: SINGLE SILICON (111) MONOCHROMATOR AND TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.7→19.77 Å / Num. obs: 26158 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.4 / Net I/σ(I): 2.4
Reflection shellResolution: 2.7→2.769 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
ARPWARP CNS REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JHR

2jhr


Resolution: 2.7→19.77 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.826 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.373
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 202-207 ARE DISORDERED. DISORDERED REGIONS COULD NOT BE MODELED DUE TO POOR DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.28871 1377 5 %RANDOM
Rwork0.20338 ---
obs0.20751 26158 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.946 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 51 198 5781
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 99 -
Rwork0.218 1881 -
obs--100 %

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