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- PDB-5ig4: Crystal structure of N. vectensis CaMKII-A hub -

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Basic information

Entry
Database: PDB / ID: 5ig4
TitleCrystal structure of N. vectensis CaMKII-A hub
ComponentsPredicted protein
KeywordsTRANSFERASE / Ca2+/CaM-dependent kinase / sea anemone / closed-ring
Function / homology
Function and homology information


protein serine/threonine kinase activity => GO:0004674 / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / calmodulin binding / neuron projection / protein serine kinase activity / ATP binding / cytoplasm
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Calcium/calmodulin-dependent protein kinase
Similarity search - Component
Biological speciesNematostella vectensis (starlet sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBhattacharyya, M. / Pappireddi, N. / Gee, C.L. / Barros, T. / Kuriyan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)NA United States
CitationJournal: Elife / Year: 2016
Title: Molecular mechanism of activation-triggered subunit exchange in Ca(2+)/calmodulin-dependent protein kinase II.
Authors: Bhattacharyya, M. / Stratton, M.M. / Going, C.C. / McSpadden, E.D. / Huang, Y. / Susa, A.C. / Elleman, A. / Cao, Y.M. / Pappireddi, N. / Burkhardt, P. / Gee, C.L. / Barros, T. / Schulman, H. ...Authors: Bhattacharyya, M. / Stratton, M.M. / Going, C.C. / McSpadden, E.D. / Huang, Y. / Susa, A.C. / Elleman, A. / Cao, Y.M. / Pappireddi, N. / Burkhardt, P. / Gee, C.L. / Barros, T. / Schulman, H. / Williams, E.R. / Kuriyan, J.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Structure summary
Revision 1.2Apr 20, 2016Group: Structure summary
Revision 1.3Jul 13, 2016Group: Data collection
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted protein
B: Predicted protein
C: Predicted protein
D: Predicted protein
E: Predicted protein
F: Predicted protein
G: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0159
Polymers114,8307
Non-polymers1842
Water2,702150
1
A: Predicted protein
B: Predicted protein
C: Predicted protein
D: Predicted protein
E: Predicted protein
F: Predicted protein
G: Predicted protein
hetero molecules

A: Predicted protein
B: Predicted protein
C: Predicted protein
D: Predicted protein
E: Predicted protein
F: Predicted protein
G: Predicted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,02918
Polymers229,66114
Non-polymers3684
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+5/21
Buried area31650 Å2
ΔGint-215 kcal/mol
Surface area76570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.466, 180.100, 179.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Predicted protein


Mass: 16404.336 Da / Num. of mol.: 7 / Fragment: UNP residues 330-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nematostella vectensis (starlet sea anemone)
Gene: v1g220432 / Production host: Escherichia coli (E. coli) / References: UniProt: A7T0H5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M potassium thiocyanate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2014 / Details: M1: parabola M2: torroid
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→47.68 Å / Num. obs: 52958 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.5 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HKX

1hkx


Resolution: 2.35→46.081 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 25.23
RfactorNum. reflection% reflection
Rfree0.2198 2602 4.91 %
Rwork0.1924 --
obs0.1939 50315 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→46.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7247 0 12 150 7409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087481
X-RAY DIFFRACTIONf_angle_d0.84510150
X-RAY DIFFRACTIONf_dihedral_angle_d12.7464426
X-RAY DIFFRACTIONf_chiral_restr0.0511154
X-RAY DIFFRACTIONf_plane_restr0.0051288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37670.32871470.32343020X-RAY DIFFRACTION93
2.3767-2.40470.33111700.30243074X-RAY DIFFRACTION96
2.4047-2.4340.34661660.30193183X-RAY DIFFRACTION98
2.434-2.46480.31051480.2943296X-RAY DIFFRACTION99
2.4648-2.49730.37311650.28863156X-RAY DIFFRACTION100
2.4973-2.53150.33122010.28743290X-RAY DIFFRACTION100
2.5315-2.56760.31711490.2693195X-RAY DIFFRACTION100
2.5676-2.60590.28441580.24253263X-RAY DIFFRACTION100
2.6059-2.64670.30091200.23873332X-RAY DIFFRACTION100
2.6467-2.690.31161820.21813171X-RAY DIFFRACTION100
2.69-2.73640.24871780.23783261X-RAY DIFFRACTION100
2.7364-2.78620.27661420.21563253X-RAY DIFFRACTION100
2.7862-2.83980.29261700.21263246X-RAY DIFFRACTION100
2.8398-2.89770.21112050.19453225X-RAY DIFFRACTION100
2.8977-2.96070.25871690.21323236X-RAY DIFFRACTION100
2.9607-3.02960.30341170.23093268X-RAY DIFFRACTION100
3.0296-3.10530.27121770.22713243X-RAY DIFFRACTION100
3.1053-3.18930.28111700.20733222X-RAY DIFFRACTION100
3.1893-3.28310.21341570.19513304X-RAY DIFFRACTION100
3.2831-3.3890.22261670.20073220X-RAY DIFFRACTION100
3.389-3.51010.23721800.20423244X-RAY DIFFRACTION100
3.5101-3.65060.19691850.18223198X-RAY DIFFRACTION100
3.6506-3.81670.20741750.1863211X-RAY DIFFRACTION100
3.8167-4.01780.20071400.17273267X-RAY DIFFRACTION100
4.0178-4.26930.17011560.14913258X-RAY DIFFRACTION99
4.2693-4.59870.15531930.12983192X-RAY DIFFRACTION100
4.5987-5.0610.14361990.13833187X-RAY DIFFRACTION100
5.061-5.79210.19451810.17673235X-RAY DIFFRACTION100
5.7921-7.29270.25381610.20543232X-RAY DIFFRACTION100
7.2927-46.09030.17911650.17073210X-RAY DIFFRACTION98

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