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- PDB-1br4: SMOOTH MUSCLE MYOSIN MOTOR DOMAIN-ESSENTIAL LIGHT CHAIN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1br4
TitleSMOOTH MUSCLE MYOSIN MOTOR DOMAIN-ESSENTIAL LIGHT CHAIN COMPLEX WITH MGADP.BEF3 BOUND AT THE ACTIVE SITE
Components(MYOSIN) x 2
KeywordsMUSCLE PROTEIN
Function / homology
Function and homology information


myosin II filament / myofibril assembly / elastic fiber assembly / myosin light chain binding / skeletal muscle myosin thick filament assembly / muscle myosin complex / myosin II binding / actomyosin / myosin filament / actomyosin structure organization ...myosin II filament / myofibril assembly / elastic fiber assembly / myosin light chain binding / skeletal muscle myosin thick filament assembly / muscle myosin complex / myosin II binding / actomyosin / myosin filament / actomyosin structure organization / myosin II complex / cardiac muscle cell development / structural constituent of muscle / microfilament motor activity / myofibril / myosin heavy chain binding / smooth muscle contraction / ADP binding / actin filament binding / actin binding / calmodulin binding / calcium ion binding / magnesium ion binding / ATP binding / cytosol / 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 / DNA repair protein XRCC4-like, C-terminal / Kinesin motor domain / Kinesin / 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 / DNA repair protein XRCC4-like, C-terminal / Kinesin motor domain / Kinesin / 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. / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 / BERYLLIUM TRIFLUORIDE ION / Myosin light polypeptide 6 / Myosin-11
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 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 27, 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 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
G: MYOSIN
H: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)444,35120
Polymers442,2818
Non-polymers2,07012
Water1448
1
A: MYOSIN
B: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0885
Polymers110,5702
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-38 kcal/mol
Surface area43730 Å2
MethodPISA
2
C: MYOSIN
D: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0885
Polymers110,5702
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-38 kcal/mol
Surface area43730 Å2
MethodPISA
3
E: MYOSIN
F: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0885
Polymers110,5702
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-38 kcal/mol
Surface area43630 Å2
MethodPISA
4
G: MYOSIN
H: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0885
Polymers110,5702
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-36 kcal/mol
Surface area43940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.320, 144.660, 147.290
Angle α, β, γ (deg.)111.21, 106.10, 92.58
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.63727, 0.75878, 0.13469), (0.76522, -0.64374, 0.00601), (0.09126, 0.09924, -0.99087)74.75926, 36.8005, 56.71992
2given(0.70766, 0.66675, 0.23381), (-0.68684, 0.72678, 0.00626), (-0.16575, -0.16502, 0.97226)-16.25359, -10.08749, 83.07092
3given(0.99662, 0.07683, -0.02907), (0.07893, -0.99368, 0.07985), (-0.02275, -0.08188, -0.99638)45.1113, 82.28576, 9.46815
4given(0.61577, 0.77684, 0.1317), (0.78282, -0.62217, 0.00974), (0.0895, 0.0971, -0.99124)73.70228, 36.52345, 56.68493
5given(0.69452, 0.67169, 0.25784), (-0.69843, 0.71546, 0.01747), (-0.17274, -0.19222, 0.96603)-16.6022, -10.1293, 83.73268
6given(0.99939, 0.02496, 0.02445), (0.0209, -0.98782, 0.15418), (0.028, -0.15357, -0.98774)46.57387, 80.63683, 12.71036

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
MYOSIN / / MDE


Mass: 93697.180 Da / Num. of mol.: 4
Fragment: CHAINS A, C, E, G, MOTOR DOMAIN, CHAINS B, D, F, H, ESSENTIAL LIGHT
Source method: isolated from a genetically manipulated source
Details: MG, ADP, BEF(3) / 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: Protein
MYOSIN / / MDE


Mass: 16873.025 Da / Num. of mol.: 4
Fragment: CHAINS A, C, E, G, MOTOR DOMAIN, CHAINS B, D, F, H, ESSENTIAL LIGHT
Source method: isolated from a genetically manipulated source
Details: MG, ADP, BEF(3) / 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: P02607, EC: 3.6.1.32

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Non-polymers , 4 types, 20 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BeF3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 277 K / pH: 7.2
Details: 1.8M AMMONIUM SULFATE 100MM HEPES PH 7.2 2MM MGADP 2MM AL(NO3)3 8MM NAF PROTEIN CONCENTRATION: 10MG/ML TEMPERATURE: 4 DEGREES CENTIGRADE, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22 mMMgADP1drop
32 mMberyllium(SIGMA)1drop
5Mammonium sulfate1reservoir
6mMHEPES1reservoir
4mM1dropNaF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.905
DetectorDetector: CCD / Date: Jul 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 3.62→20 Å / Num. obs: 75979 / % possible obs: 95.6 % / Redundancy: 6.3 % / Rsym value: 0.111 / Net I/σ(I): 13.7
Reflection shellResolution: 3.62→3.9 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.331 / % possible all: 94.2
Reflection
*PLUS
Num. measured all: 478668 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 94.2 % / Rmerge(I) obs: 0.331

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SMOOTH MUSCLE MOTOR DOMAIN

Resolution: 3.62→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
Rfree0.352 -5 %RANDOM
Rwork0.277 ---
obs0.277 72931 95.7 %-
Displacement parametersBiso mean: 48.9 Å2
Refine analyzeLuzzati coordinate error free: 0.7 Å
Refinement stepCycle: LAST / Resolution: 3.62→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29824 0 136 8 29968
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
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_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6

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