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- PDB-2bdw: Crystal Structure of the Auto-Inhibited Kinase Domain of Calcium/... -

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Basic information

Entry
Database: PDB / ID: 2bdw
TitleCrystal Structure of the Auto-Inhibited Kinase Domain of Calcium/Calmodulin Activated Kinase II
ComponentsHypothetical protein K11E8.1dHypothesis
KeywordsTRANSFERASE / kinase / calmodulin activated
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 / peptidyl-threonine phosphorylation / MAPK cascade / perikaryon / peptidyl-serine phosphorylation / transmembrane transporter binding / calmodulin binding / neuron projection / phosphorylation / protein 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 / Resolution: 1.8 Å
AuthorsRosenberg, O.S. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Structure of the Autoinhibited Kinase Domain of CaMKII and SAXS Analysis of the Holoenzyme
Authors: Rosenberg, O.S. / Deindl, S. / Sung, R.-J. / Nairn, A.C. / Kuriyan, J.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein K11E8.1d
B: Hypothetical protein K11E8.1d


Theoretical massNumber of molelcules
Total (without water)81,2592
Polymers81,2592
Non-polymers00
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-12 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.121, 77.104, 119.520
Angle α, β, γ (deg.)90.00, 96.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein K11E8.1d / Hypothesis


Mass: 40629.309 Da / Num. of mol.: 2 / Fragment: auto-inhibited kinase domain fragment / Mutation: D135N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata)
Gene: Ca2+/calmodulin-dependent protein kinase; unc-43 (K11E8.1d)
Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: Q9NG91, UniProt: O62305*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.6 M sodium malonate, 1.5 % 1,2,3-heptanetriol, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→45.8 Å / Num. all: 76218 / Num. obs: 73357 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 18.9 Å2
Reflection shellResolution: 1.8→1.91 Å / % possible all: 83.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2phk

2phk


Resolution: 1.8→45.8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 7448 -RANDOM
Rwork0.216 ---
all0.216 ---
obs0.216 73357 95.6 %-
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.96 Å20 Å2-2.08 Å2
2---7.33 Å20 Å2
3---0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4923 0 0 431 5354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.75

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