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- PDB-4fgb: Crystal structure of human calcium/calmodulin-dependent protein k... -

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Basic information

Entry
Database: PDB / ID: 4fgb
TitleCrystal structure of human calcium/calmodulin-dependent protein kinase I apo form
ComponentsCalcium/calmodulin-dependent protein kinase type 1
KeywordsTRANSFERASE / CaMK / calmodulin / autoinhibition / regulation mechanism / kinase
Function / homology
Function and homology information


positive regulation of syncytium formation by plasma membrane fusion / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / Ca2+/calmodulin-dependent protein kinase / regulation of protein binding / nucleocytoplasmic transport / calcium/calmodulin-dependent protein kinase activity / Activation of RAC1 downstream of NMDARs / positive regulation of dendritic spine development / positive regulation of muscle cell differentiation ...positive regulation of syncytium formation by plasma membrane fusion / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / Ca2+/calmodulin-dependent protein kinase / regulation of protein binding / nucleocytoplasmic transport / calcium/calmodulin-dependent protein kinase activity / Activation of RAC1 downstream of NMDARs / positive regulation of dendritic spine development / positive regulation of muscle cell differentiation / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of protein export from nucleus / negative regulation of protein binding / positive regulation of protein serine/threonine kinase activity / positive regulation of neuron projection development / regulation of protein localization / nervous system development / cell differentiation / calmodulin binding / intracellular signal transduction / cell cycle / protein phosphorylation / protein serine kinase activity / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol
Similarity search - Function
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. ...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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZha, M. / Zhong, C. / Ou, Y. / Wang, J. / Han, L. / Ding, J.
CitationJournal: Plos One / Year: 2012
Title: Crystal structures of human CaMKIalpha reveal insights into the regulation mechanism of CaMKI.
Authors: Zha, M. / Zhong, C. / Ou, Y. / Han, L. / Wang, J. / Ding, J.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent protein kinase type 1


Theoretical massNumber of molelcules
Total (without water)36,4251
Polymers36,4251
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.046, 67.700, 56.138
Angle α, β, γ (deg.)90.000, 99.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase type 1 / CaM kinase I / CaM-KI / CaM kinase I alpha / CaMKI-alpha


Mass: 36424.559 Da / Num. of mol.: 1 / Fragment: residues 1-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK1 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14012, Ca2+/calmodulin-dependent protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.0 M (NH4)2SO4, 100 mM bicine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.964 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.6→55.05 Å / Num. all: 9256 / % possible obs: 88.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.4
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FG7

4fg7


Resolution: 2.6→55.05 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.847 / Occupancy max: 1 / Occupancy min: 1 / SU B: 30.377 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.422 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2994 470 5.1 %RANDOM
Rwork0.2479 ---
obs0.2505 9219 88.21 %-
all-9256 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.18 Å2 / Biso mean: 32.7233 Å2 / Biso min: 11.22 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å20 Å20.77 Å2
2---1.23 Å20 Å2
3----3.06 Å2
Refinement stepCycle: LAST / Resolution: 2.6→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 0 58 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222278
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.9613087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.96724.808104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40715388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.978158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211724
X-RAY DIFFRACTIONr_mcbond_it0.4981.51405
X-RAY DIFFRACTIONr_mcangle_it0.79222254
X-RAY DIFFRACTIONr_scbond_it1.6523873
X-RAY DIFFRACTIONr_scangle_it2.3884.5833
X-RAY DIFFRACTIONr_rigid_bond_restr1.1132278
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 41 -
Rwork0.261 713 -
all-754 -
obs--97.92 %

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