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- PDB-3kf9: Crystal structure of the SdCen/skMLCK complex -

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Basic information

Entry
Database: PDB / ID: 3kf9
TitleCrystal structure of the SdCen/skMLCK complex
Components
  • Caltractin
  • Myosin light chain kinase 2, skeletal/cardiac muscle
KeywordsCELL CYCLE/CALCIUM-BINDING PROTEIN / centrin / myosin light chain kinase / Cell cycle / Cell division / Mitosis / Calmodulin-binding / CELL CYCLE-CALCIUM-BINDING PROTEIN complex
Function / homology
Function and homology information


skeletal muscle satellite cell differentiation / regulation of muscle filament sliding / myosin-light-chain kinase / myosin light chain kinase activity / myosin light chain binding / neuromuscular synaptic transmission / cardiac muscle tissue morphogenesis / calcium/calmodulin-dependent protein kinase activity / skeletal muscle cell differentiation / cardiac muscle contraction ...skeletal muscle satellite cell differentiation / regulation of muscle filament sliding / myosin-light-chain kinase / myosin light chain kinase activity / myosin light chain binding / neuromuscular synaptic transmission / cardiac muscle tissue morphogenesis / calcium/calmodulin-dependent protein kinase activity / skeletal muscle cell differentiation / cardiac muscle contraction / striated muscle contraction / centriole / sarcomere / peptidyl-threonine phosphorylation / mitotic cell cycle / protein autophosphorylation / calmodulin binding / cell division / calcium ion binding / synapse / positive regulation of gene expression / ATP binding / nucleus / cytoplasm
Similarity search - Function
Myosin light chain kinase 2, catalytic domain / ATP-dependent RNA helicase DEAD-box, conserved site / : / 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. ...Myosin light chain kinase 2, catalytic domain / ATP-dependent RNA helicase DEAD-box, conserved site / : / 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 / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Caltractin / Myosin light chain kinase 2, skeletal/cardiac muscle
Similarity search - Component
Biological speciesScherffelia dubia (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRadu, L. / Assairi, L. / Blouquit, Y. / Durand, D. / Miron, S. / Charbonnier, J.B. / Craescu, C.T.
CitationJournal: To be Published
Title: Structural features of the complexes formed by Scherffelia dubia centrin
Authors: Radu, L. / Miron, S. / Durand, D. / Assairi, L. / Blouquit, Y. / Charbonnier, J.B.
History
DepositionOct 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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.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_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

Downloads & links

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Assembly

Deposited unit
A: Caltractin
B: Myosin light chain kinase 2, skeletal/cardiac muscle
C: Caltractin
D: Myosin light chain kinase 2, skeletal/cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,05212
Polymers39,7314
Non-polymers3218
Water1,24369
1
A: Caltractin
B: Myosin light chain kinase 2, skeletal/cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0266
Polymers19,8652
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-65 kcal/mol
Surface area9560 Å2
MethodPISA
2
C: Caltractin
D: Myosin light chain kinase 2, skeletal/cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0266
Polymers19,8652
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-78 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.750, 67.750, 129.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
/ NCS ensembles :
ID
1
2

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Components

#1: Protein Caltractin / Centrin


Mass: 17221.316 Da / Num. of mol.: 2 / Fragment: UNP residues 20-168 out of 168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scherffelia dubia (plant) / Plasmid: PET24A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06827
#2: Protein/peptide Myosin light chain kinase 2, skeletal/cardiac muscle / MLCK2


Mass: 2644.172 Da / Num. of mol.: 2 / Fragment: UNP residues 566-587 out of 596 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. THIS SEQUENCE OCCURS IN HOMO SAPIENS
References: UniProt: Q9H1R3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPEG 2000, Nacacodylate 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2009
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 10844 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 10.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1576 / Rsym value: 0.235 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QTX

1qtx


Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.819 / SU B: 28.577 / SU ML: 0.286 / Cross valid method: THROUGHOUT / σ(F): 2.5 / σ(I): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29021 525 4.8 %RANDOM
Rwork0.20002 ---
obs0.20427 10318 93.04 %-
all-11661 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.735 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2--1.5 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 8 69 2808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222759
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.973659
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2355337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60325.07142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27215581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.251521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022035
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4741.51681
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92922674
X-RAY DIFFRACTIONr_scbond_it1.75731078
X-RAY DIFFRACTIONr_scangle_it2.9794.5985
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
111172medium positional0.410.5
22177medium positional0.460.5
111172medium thermal0.632
22177medium thermal0.592
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 38 -
Rwork0.234 762 -
obs--95.24 %
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)
12.7299-0.6047-0.83750.86910.52761.2384-0.0098-0.04320.11720.0724-0.0021-0.0338-0.0336-0.02650.01190.0816-0.00540.00050.0066-0.00960.01620.6609-0.79127.3821
27.1843-4.5408-0.41158.042.58782.05150.16260.0275-0.0619-0.2739-0.29430.1994-0.1263-0.01170.13180.126-0.05310.02620.083-0.01050.0467-1.01520.16996.1983
33.4364-0.6028-0.42320.750.25111.0643-0.0247-0.1075-0.29440.01350.02480.0543-0.019-0.0111-0.00010.088-0.0083-0.00130.0527-0.00340.0589.20057.305736.2388
411.62176.3374-4.157612.2871-7.51688.2663-0.1399-0.3237-0.23090.44880.42750.0008-0.5413-0.5567-0.28760.15530.03680.03540.2235-0.04160.077211.01199.368136.3691
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 168
2X-RAY DIFFRACTION2B1 - 22
3X-RAY DIFFRACTION3C20 - 168
4X-RAY DIFFRACTION4D2 - 22

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