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- PDB-3kk9: CaMKII Substrate Complex B -

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Basic information

Entry
Database: PDB / ID: 3kk9
TitleCaMKII Substrate Complex B
ComponentsCalcium/calmodulin dependent protein kinase II
KeywordsTRANSFERASE / CaMKII / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase
Function / homology
Function and homology information


medium-term memory / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / Ion homeostasis / Ca2+ pathway / HSF1-dependent transactivation / serotonin biosynthetic process / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / axon cytoplasm ...medium-term memory / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / Ion homeostasis / Ca2+ pathway / HSF1-dependent transactivation / serotonin biosynthetic process / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / axon cytoplasm / MAPK cascade / perikaryon / transmembrane transporter binding / calmodulin binding / neuron projection / phosphorylation / protein serine kinase activity / positive regulation of gene expression / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calcium/calmodulin-dependent protein kinase type II / Calcium/calmodulin-dependent protein kinase type II
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.206 Å
AuthorsKuriyan, J. / Chao, L.H. / Pellicena, P. / Deindl, S. / Barclay, L.A. / Schulman, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation.
Authors: Chao, L.H. / Pellicena, P. / Deindl, S. / Barclay, L.A. / Schulman, H. / Kuriyan, J.
History
DepositionNov 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium/calmodulin dependent protein kinase II


Theoretical massNumber of molelcules
Total (without water)32,0031
Polymers32,0031
Non-polymers00
Water00
1
A: Calcium/calmodulin dependent protein kinase II

A: Calcium/calmodulin dependent protein kinase II


Theoretical massNumber of molelcules
Total (without water)64,0072
Polymers64,0072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.708, 60.470, 70.243
Angle α, β, γ (deg.)90.000, 93.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calcium/calmodulin dependent protein kinase II


Mass: 32003.350 Da / Num. of mol.: 1 / Fragment: CaMKII kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-43, K11E8.1, K11E8.1d / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U6Q0, UniProt: O62305*PLUS

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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: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 15% 2-methyl-2,4-pentanediol, .1M potassium chloride, 5mM magnesium suflate, 50mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 5292 / Num. obs: 5171 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.127 / Net I/σ(I): 9.93
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 463 / Rsym value: 0.399 / % possible all: 87.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.85 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.21 Å45.78 Å
Translation3.21 Å45.78 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASER2.1.1phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.206→45.782 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.68 / SU ML: 0.76 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.329 236 4.58 %RANDOM
Rwork0.27 ---
obs0.272 5153 97.5 %-
all-5292 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.034 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso max: 195.44 Å2 / Biso mean: 91.219 Å2 / Biso min: 57.85 Å2
Baniso -1Baniso -2Baniso -3
1-65.114 Å2-0 Å217.363 Å2
2---37.622 Å2-0 Å2
3----27.492 Å2
Refinement stepCycle: LAST / Resolution: 3.206→45.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 0 0 2204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042257
X-RAY DIFFRACTIONf_angle_d0.7983062
X-RAY DIFFRACTIONf_chiral_restr0.053336
X-RAY DIFFRACTIONf_plane_restr0.003392
X-RAY DIFFRACTIONf_dihedral_angle_d15.927817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.206-4.0380.3861170.312378249595
4.038-45.7870.2991190.24925392658100
Refinement TLS params.Method: refined / Origin x: -13.7108 Å / Origin y: -16.3141 Å / Origin z: -19.2794 Å
111213212223313233
T0.035 Å2-0.0078 Å20.0312 Å2-0.3536 Å20.0069 Å2--0.2581 Å2
L1.1008 °20.0876 °20.4936 °2-3.1507 °2-0.3188 °2--2.2915 °2
S-0.115 Å °0.4115 Å °-0.1052 Å °-0.1861 Å °-0.0365 Å °0.025 Å °-0.2236 Å °0.1134 Å °-0.0547 Å °
Refinement TLS groupSelection details: all

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