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- PDB-2jc6: Crystal structure of human calmodulin-dependent protein kinase 1D -

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Basic information

Entry
Database: PDB / ID: 2jc6
TitleCrystal structure of human calmodulin-dependent protein kinase 1D
ComponentsCALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE 1D
KeywordsTRANSFERASE / ATP-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION
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
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
Chem-QPP / Calcium/calmodulin-dependent protein kinase type 1D
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDebreczeni, J.E. / Rellos, P. / Fedorov, O. / Niesen, F.H. / Bhatia, C. / Shrestha, L. / Salah, E. / Smee, C. / Colebrook, S. / Berridge, G. ...Debreczeni, J.E. / Rellos, P. / Fedorov, O. / Niesen, F.H. / Bhatia, C. / Shrestha, L. / Salah, E. / Smee, C. / Colebrook, S. / Berridge, G. / Gileadi, O. / Bunkoczi, G. / Ugochukwu, E. / Pike, A.C.W. / von Delft, F. / Knapp, S. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.
CitationJournal: To be Published
Title: Crystal Structure of Human Calmodulin-Dependent Protein Kinase 1D
Authors: Debreczeni, J.E. / Rellos, P. / Fedorov, O. / Niesen, F.H. / Bhatia, C. / Shrestha, L. / Salah, E. / Smee, C. / Colebrook, S. / Berridge, G. / Gileadi, O. / Bunkoczi, G. / Ugochukwu, E. / ...Authors: Debreczeni, J.E. / Rellos, P. / Fedorov, O. / Niesen, F.H. / Bhatia, C. / Shrestha, L. / Salah, E. / Smee, C. / Colebrook, S. / Berridge, G. / Gileadi, O. / Bunkoczi, G. / Ugochukwu, E. / Pike, A.C.W. / von Delft, F. / Knapp, S. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.
History
DepositionDec 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE 1D
C: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3834
Polymers75,7802
Non-polymers6032
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-21.4 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.640, 93.060, 101.860
Angle α, β, γ (deg.)90.00, 96.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 222
2114C3 - 222
1214A233 - 313
2214C233 - 313

NCS oper: (Code: given
Matrix: (-0.99999, 0.00435, 0.00247), (0.00467, -0.63478, -0.77268), (-0.00179, -0.77268, 0.63479)
Vector: -4.30173, -126.35943, -59.53677)

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Components

#1: Protein CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE 1D / CALMODULIN-DEPENDENT PROTEIN KINASE 1D / CAM KINASE ID / CAM KINASE I DELTA / CAMKI-DELTA / CAM-KI ...CALMODULIN-DEPENDENT PROTEIN KINASE 1D / CAM KINASE ID / CAM KINASE I DELTA / CAMKI-DELTA / CAM-KI DELTA / CAMKI DELTA / CAMK1D / CAMKI-LIKE PROTEIN KINASE / CKLIK


Mass: 37890.125 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-ROSETTA
References: UniProt: Q8IU85, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-QPP / N-(5-METHYL-1H-PYRAZOL-3-YL)-2-PHENYLQUINAZOLIN-4-AMINE / 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE


Mass: 301.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H15N5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.59 Å3/Da / Density % sol: 52 %
Crystal growDetails: 0.1M CITRATE PH 5.6, 20% ISOPROPANOL, 20% PEG 4K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9796
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2006 / Details: MIRROR
RadiationMonochromator: SI 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→42.2 Å / Num. obs: 29986 / % possible obs: 91.6 % / Observed criterion σ(I): 2 / Redundancy: 3.47 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.17
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.56 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A06

1a06


Resolution: 2.3→101.02 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.898 / SU B: 13.019 / SU ML: 0.164 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1514 5.1 %RANDOM
Rwork0.186 ---
obs0.189 28455 91.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å2-0.23 Å2
2--0.12 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→101.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4367 0 46 188 4601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224549
X-RAY DIFFRACTIONr_bond_other_d0.0040.023044
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9656169
X-RAY DIFFRACTIONr_angle_other_deg0.9173.0017399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2915555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5424.519208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51915754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3451520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02920
X-RAY DIFFRACTIONr_nbd_refined0.1890.2848
X-RAY DIFFRACTIONr_nbd_other0.190.23012
X-RAY DIFFRACTIONr_nbtor_refined0.180.22158
X-RAY DIFFRACTIONr_nbtor_other0.0890.22360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.18232906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.33954446
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.69772014
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.199111720
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3518 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.250.5
medium thermal0.922
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 117
Rwork0.213 2276
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.94362.20910.7964.55353.1373.06230.2721-0.43930.33270.3328-0.28170.21870.065-0.09170.0096-0.0407-0.0858-0.0001-0.0604-0.03580.0132-8.105-74.783-29.44
21.8026-0.155-0.04721.19840.15421.17090.1037-0.0897-0.0454-0.0537-0.05070.0150.08930.0229-0.053-0.1105-0.084-0.005-0.0597-0.0147-0.1081.907-97.572-44.083
31.6125-0.5763-0.30413.77220.24311.29210.0726-0.0783-0.07850.2252-0.06240.09020.2036-0.0051-0.0102-0.0498-0.0744-0.0237-0.0622-0.0115-0.10893.643-56.113-20.569
42.86770.1224-0.07461.37410.3921.11040.0978-0.21210.347-0.0035-0.0430.0224-0.15850.02-0.0548-0.0835-0.087-0.0023-0.0819-0.0321-0.0237-6.763-30.25-12.18
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 101
2X-RAY DIFFRACTION2A102 - 313
3X-RAY DIFFRACTION3C11 - 101
4X-RAY DIFFRACTION4C102 - 313

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