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- PDB-2bl0: Physarum polycephalum myosin II regulatory domain -

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Basic information

Entry
Database: PDB / ID: 2bl0
TitlePhysarum polycephalum myosin II regulatory domain
Components
  • (MYOSIN REGULATORY LIGHT CHAIN) x 2
  • MAJOR PLASMODIAL MYOSIN HEAVY CHAIN
KeywordsMUSCLE PROTEIN / SLIME MOULD / EF-HAND / MYOSIN
Function / homology
Function and homology information


myosin complex / cytoskeletal motor activity / actin filament binding / calcium ion binding / ATP binding
Similarity search - Function
Myosin, subunit A / Myosin, subunit A / : / Myosin tail / Myosin tail / EF hand / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Myosin, subunit A / Myosin, subunit A / : / Myosin tail / Myosin tail / EF hand / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / 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 / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Few Secondary Structures / Irregular / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myosin regulatory light chain / Myosin regulatory light chain / Major plasmodial myosin heavy chain
Similarity search - Component
Biological speciesPHYSARUM POLYCEPHALUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.75 Å
AuthorsDebreczeni, J.E. / Farkas, L. / Harmat, V. / Nyitray, L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Evidence for Non-Canonical Binding of Ca2+ to a Canonical EF-Hand of a Conventional Myosin.
Authors: Debreczeni, J.E. / Farkas, L. / Harmat, V. / Hetenyi, C. / Hajdu, I. / Zavodszky, P. / Kohama, K. / Nyitray, L.
History
DepositionFeb 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
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_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_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_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR PLASMODIAL MYOSIN HEAVY CHAIN
B: MYOSIN REGULATORY LIGHT CHAIN
C: MYOSIN REGULATORY LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7915
Polymers39,7113
Non-polymers802
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.574, 70.858, 97.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MAJOR PLASMODIAL MYOSIN HEAVY CHAIN / PHYSARUM POLYCEPHALUM MYOSIN II HEAVY CHAIN


Mass: 7577.932 Da / Num. of mol.: 1 / Fragment: REGULATORY DOMAIN, RESIDUES 778-840
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSARUM POLYCEPHALUM (eukaryote) / Production host: ESCHERICIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9BJD3, EC: 3.6.1.32
#2: Protein MYOSIN REGULATORY LIGHT CHAIN / PHYSARUM POLYCEPHALUM MYOSIN II ESSENTIAL LIGHT CHAIN / CALCIUM-BINDING LIGHT CHAIN


Mass: 15937.804 Da / Num. of mol.: 1 / Fragment: REGULATORY DOMAIN, RESIDUES 1-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSARUM POLYCEPHALUM (eukaryote) / Production host: ESCHERICIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P08053, EC: 3.6.1.32
#3: Protein MYOSIN REGULATORY LIGHT CHAIN / PHYSARUM POLYCEPHALUM MYOSIN II REGULATORY LIGHT CHAIN


Mass: 16195.120 Da / Num. of mol.: 1 / Fragment: REGULATORY DOMAIN, RESIDUES 14-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSARUM POLYCEPHALUM (eukaryote) / Production host: ESCHERICIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8WSQ4, EC: 3.6.1.32
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.24 Å3/Da / Density % sol: 44.56 %
Crystal growDetails: PROTEIN SOL: 8.5 MG/ML PHYS RD IN 10 MM TRIS PH 7.6, 10 MM CACL2, RESERVOIR SOL: 20% PEG4000, 0.5 M CAAC PH 4.6, 0.1 M NH4AC, 0.05 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→57.7 Å / Num. obs: 39847 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
DMphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.75→57.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.88 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1990 5 %RANDOM
Rwork0.219 ---
obs0.221 37613 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--2.08 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.75→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 2 230 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222895
X-RAY DIFFRACTIONr_bond_other_d0.0020.022630
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9553897
X-RAY DIFFRACTIONr_angle_other_deg0.8336150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9965347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023200
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02592
X-RAY DIFFRACTIONr_nbd_refined0.2130.2685
X-RAY DIFFRACTIONr_nbd_other0.2340.22946
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.21622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6531.51745
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21322812
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.92531150
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2034.51085
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 139
Rwork0.278 2754
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.02090.06990.42440.36210.61272.023-0.1032-0.10620.03810.0082-0.18130.08890.0138-0.24060.28450.1968-0.0274-0.02230.2543-0.03510.214224.537531.812248.0305
22.26061.0728-0.29881.1245-0.70961.6667-0.06520.0421-0.0092-0.0370.0097-0.0088-0.0547-0.0060.05550.21750.008-0.03360.17930.01430.20538.972343.547655.9142
30.6075-0.5094-0.49721.5896-0.64951.4788-0.0949-0.0803-0.00140.03420.09160.0694-0.0793-0.0230.00330.20470.0481-0.01040.21170.02650.223133.438832.31777.635
43.81931.3441-0.69021.4966-0.35981.4118-0.1738-0.00820.0408-0.14830.18180.00420.0084-0.0626-0.0080.2427-0.0328-0.01920.1665-0.00710.16221.58120.978917.939
55.00760.41332.74893.17380.50915.7803-0.0532-0.97480.40030.184-0.49280.1760.2083-1.48950.5460.0857-0.08890.04320.5259-0.26860.137211.436233.264943.0717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A778 - 840
2X-RAY DIFFRACTION2B1 - 71
3X-RAY DIFFRACTION3B72 - 145
4X-RAY DIFFRACTION4C13 - 86
5X-RAY DIFFRACTION5C87 - 154

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