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- PDB-6qp5: Apo Human Calcium/Calmodulin-dependent kinase type 1D -

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Basic information

Entry
Database: PDB / ID: 6qp5
TitleApo Human Calcium/Calmodulin-dependent kinase type 1D
ComponentsCalcium/calmodulin-dependent protein kinase type 1D
KeywordsTRANSFERASE / Kinase / CAMK1D / Apo / unphosphorylated
Function / homology
Function and homology information


regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / positive regulation of neutrophil chemotaxis / calmodulin-dependent protein kinase activity / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development / nervous system development ...regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / positive regulation of neutrophil chemotaxis / calmodulin-dependent protein kinase activity / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development / nervous system development / calmodulin binding / inflammatory response / positive regulation of apoptotic process / phosphorylation / protein serine kinase activity / negative regulation of apoptotic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
Calcium/calmodulin-dependent protein kinase type 1D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSorrell, F.J. / Knapp, S.
CitationJournal: To Be Published
Title: Apo Human Calcium/Calmodulin-dependent kinase type 1D
Authors: Sorrell, F.J. / Knapp, S.
History
DepositionFeb 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0155
Polymers36,6991
Non-polymers3164
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-14 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.110, 45.790, 107.931
Angle α, β, γ (deg.)90.000, 105.800, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase type 1D / CaM kinase I delta / CaMKID / CaMKI-like protein kinase / CKLiK


Mass: 36698.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK1D, CAMKID / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IU85, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG4000 -- 0.2M lithium sulfate -- 0.1M tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→34.62 Å / Num. obs: 24548 / % possible obs: 99.1 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.041 / Rrim(I) all: 0.088 / Net I/σ(I): 10.5 / Num. measured all: 107590 / Scaling rejects: 117
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.451 / Num. unique obs: 1444 / CC1/2: 0.487 / Rpim(I) all: 0.276 / Rrim(I) all: 0.532 / % possible all: 93.3

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
PHASERphasing
PHENIX1.9_1682refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JC6

2jc6


Resolution: 1.9→34.62 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.2272 1257 5.13 %
Rwork0.1919 --
obs0.1937 24524 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.65 Å2 / Biso mean: 35.1966 Å2 / Biso min: 13.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 18 194 2293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042159
X-RAY DIFFRACTIONf_angle_d0.7932923
X-RAY DIFFRACTIONf_chiral_restr0.032321
X-RAY DIFFRACTIONf_plane_restr0.004374
X-RAY DIFFRACTIONf_dihedral_angle_d11.656782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.9740.31661240.2646244995
1.974-2.06380.27231340.2238259599
2.0638-2.17260.22091580.1982253699
2.1726-2.30870.24591480.1939257699
2.3087-2.4870.23391330.1923257099
2.487-2.73710.24441340.1891261499
2.7371-3.1330.22831400.18682604100
3.133-3.94630.2211590.1772614100

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