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- PDB-1br2: SMOOTH MUSCLE MYOSIN MOTOR DOMAIN COMPLEXED WITH MGADP.ALF4 -

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Basic information

Entry
Database: PDB / ID: 1br2
TitleSMOOTH MUSCLE MYOSIN MOTOR DOMAIN COMPLEXED WITH MGADP.ALF4
ComponentsMYOSIN
KeywordsMUSCLE PROTEIN
Function / homology
Function and homology information


elastic fiber assembly / myofibril assembly / skeletal muscle myosin thick filament assembly / myosin light chain binding / myosin II binding / muscle myosin complex / myosin filament / actomyosin structure organization / myosin II complex / cardiac muscle cell development ...elastic fiber assembly / myofibril assembly / skeletal muscle myosin thick filament assembly / myosin light chain binding / myosin II binding / muscle myosin complex / myosin filament / actomyosin structure organization / myosin II complex / cardiac muscle cell development / structural constituent of muscle / microfilament motor activity / myofibril / smooth muscle contraction / ADP binding / actin filament binding / actin binding / calmodulin binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal ...Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / DNA repair protein XRCC4-like, C-terminal / 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. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Arc Repressor Mutant, subunit A / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / Myosin-11
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDominguez, R. / Trybus, K.M. / Cohen, C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of a vertebrate smooth muscle myosin motor domain and its complex with the essential light chain: visualization of the pre-power stroke state.
Authors: Dominguez, R. / Freyzon, Y. / Trybus, K.M. / Cohen, C.
History
DepositionAug 26, 1998Processing site: BNL
Revision 1.0Sep 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...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.process_site / _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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOSIN
B: MYOSIN
C: MYOSIN
D: MYOSIN
E: MYOSIN
F: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)545,97524
Polymers542,6486
Non-polymers3,32718
Water21612
1
A: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9964
Polymers90,4411
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9964
Polymers90,4411
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9964
Polymers90,4411
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9964
Polymers90,4411
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9964
Polymers90,4411
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9964
Polymers90,4411
Non-polymers5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.010, 107.670, 188.310
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9976, 0.06865, -0.00888), (0.06899, 0.99659, -0.04529), (0.00574, -0.0458, -0.99893)129.05473, 51.34279, 98.1799
2given(-0.99067, 0.1001, -0.09251), (0.01566, -0.5906, -0.80681), (-0.1354, -0.80073, 0.58352)84.21188, 79.82545, 108.69299
3given(-0.98429, 0.14462, -0.10131), (-0.15426, -0.42508, 0.89191), (0.08592, 0.89353, 0.44071)37.79606, 24.29972, -17.58553
4given(0.97735, -0.19164, 0.08978), (-0.1637, -0.41575, 0.89463), (-0.13412, -0.88906, -0.4377)98.94315, 77.70154, 110.75905
5given(0.9969, -0.0528, 0.05836), (0.01698, -0.57982, -0.81457), (0.07685, 0.81303, -0.57713)44.46971, 133.12106, -10.85735

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Components

#1: Protein
MYOSIN


Mass: 90441.414 Da / Num. of mol.: 6 / Fragment: MOTOR DOMAIN
Source method: isolated from a genetically manipulated source
Details: LIGANDS MG, ADP, ALF(4) / Source: (gene. exp.) Gallus gallus (chicken) / Tissue: SMOOTH MUSCLE / Cell line: SF9 / Organ: GIZZARD / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10587, EC: 3.6.1.32
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / pH: 6.8
Details: 12% PEG8000 100MM IMIDAZOLE PH 6.8 150MM CACL2 2MM MGADP 2MM AL(NO3)3 8MM NAF PROTEIN CONCENTRATION: 10MG/ML TEMPERATURE: 4 DEGREES CENTIGRADE, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22 mMMgADP1drop
32 mM1dropAlNO3)
412 %PEG80001reservoir
5150 mM1reservoirCaCl2
6100 mMimidazole1reservoir
78 mM1dropNaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorDetector: CCD / Date: Jan 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 99071 / % possible obs: 83.7 % / Redundancy: 3.3 % / Rsym value: 0.072 / Net I/σ(I): 28
Reflection shellResolution: 2.9→3.12 Å / Redundancy: 3 % / Mean I/σ(I) obs: 14.5 / Rsym value: 0.215 / % possible all: 67.7
Reflection
*PLUS
Num. measured all: 326933 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 67.7 % / Rmerge(I) obs: 0.215

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MND

1mnd


Resolution: 2.9→10 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 -5 %RANDOM
Rwork0.232 ---
obs0.232 96444 83.1 %-
Displacement parametersBiso mean: 41.5 Å2
Refine analyzeLuzzati coordinate error free: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31674 0 210 12 31896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6

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