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- PDB-2o5g: Calmodulin-smooth muscle light chain kinase peptide complex -

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Basic information

Entry
Database: PDB / ID: 2o5g
TitleCalmodulin-smooth muscle light chain kinase peptide complex
Components
  • Calmodulin
  • Smooth muscle Myosin light chain kinase peptide
KeywordsMETAL BINDING PROTEIN / protein-peptide complex
Function / homology
Function and homology information


CH domain binding / tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / muscle structure development / myosin binding / cleavage furrow / stress fiber / disordered domain specific binding / lamellipodium ...CH domain binding / tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / muscle structure development / myosin binding / cleavage furrow / stress fiber / disordered domain specific binding / lamellipodium / calmodulin binding / calcium ion binding / protein-containing complex / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / : / : / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / Recoverin; domain 1 / Fibronectin type III domain / Fibronectin type 3 domain ...Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / : / : / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / Recoverin; domain 1 / Fibronectin type III domain / Fibronectin type 3 domain / EF-hand domain pair / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / 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 / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myosin light chain kinase, smooth muscle / Calmodulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsValentine, K.G. / Ng, H.L. / Schneeweis, J.K. / Kranz, J.K. / Frederick, K.K. / Alber, T. / Wand, A.J.
CitationJournal: To be Published
Title: Ultrahigh resolution crystal structure of calmodulin-smooth muscle light kinase peptide complex
Authors: Valentine, K.G. / Ng, H.L. / Schneeweis, J.K. / Kranz, J.K. / Frederick, K.K. / Alber, T. / Wand, A.J.
History
DepositionDec 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Smooth muscle Myosin light chain kinase peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2007
Polymers18,9442
Non-polymers2565
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-84 kcal/mol
Surface area9290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)28.861, 56.894, 44.760
Angle α, β, γ (deg.)90.00, 97.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALM / Plasmid: pET-15b, modified / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62149
#2: Protein/peptide Smooth muscle Myosin light chain kinase peptide


Mass: 2222.646 Da / Num. of mol.: 1 / Fragment: calmodulin binding domain / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence can be naturally found in Gallus gallus (Chicken)
References: UniProt: P11799
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 400, 0.2 M sodium acetate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.008
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.08→56.796 Å / Num. obs: 61087 / Redundancy: 2.8 % / Biso Wilson estimate: 7.925 Å2 / Rsym value: 0.056 / Net I/σ(I): 11.2
Reflection shellResolution: 1.08→1.14 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 8739 / Rsym value: 0.227

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-IceIcedata collection
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.438 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1648 3092 5.1 %RANDOM
Rwork0.14235 ---
obs0.14351 57946 99.34 %-
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: 11.053 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.35 Å2
2--0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.08→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 9 246 1569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221380
X-RAY DIFFRACTIONr_bond_other_d0.0020.021237
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9621847
X-RAY DIFFRACTIONr_angle_other_deg1.00132901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.345164
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_restr0.1180.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021523
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02263
X-RAY DIFFRACTIONr_nbd_refined0.2470.2378
X-RAY DIFFRACTIONr_nbd_other0.2420.21474
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.2767
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.219
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.651.5827
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.46221335
X-RAY DIFFRACTIONr_scbond_it3.3153553
X-RAY DIFFRACTIONr_scangle_it4.9634.5512
X-RAY DIFFRACTIONr_rigid_bond_restr1.48221380
X-RAY DIFFRACTIONr_sphericity_free12.2275250
X-RAY DIFFRACTIONr_sphericity_bonded5.13851367
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.24 188
Rwork0.212 4192

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