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- PDB-8bfs: Crystal structure of human calmodulin-dependent protein kinase 1D... -

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Basic information

Entry
Database: PDB / ID: 8bfs
TitleCrystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) in complex with FZ326
ComponentsCalcium/calmodulin-dependent protein kinase type 1D
KeywordsTRANSFERASE / CAMK1D / Kinase
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 / calcium/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 / calcium/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 / protein serine kinase activity / negative regulation of apoptotic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
3~{H}-pyrrolo[2,3-c]isoquinolin-5-amine / Calcium/calmodulin-dependent protein kinase type 1D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKraemer, A. / Zhu, W.F. / Hernandez-Olmos, V. / Proschak, E. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) in complex with FZ326
Authors: Kraemer, A. / Zhu, W.F. / Hernandez-Olmos, V. / Proschak, E. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionOct 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Calcium/calmodulin-dependent protein kinase type 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,94712
Polymers42,9731
Non-polymers97411
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-56 kcal/mol
Surface area13600 Å2
Unit cell
Length a, b, c (Å)57.809, 45.948, 108.535
Angle α, β, γ (deg.)90.000, 103.960, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-576-

HOH

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Components

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


Mass: 42972.801 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-QNR / 3~{H}-pyrrolo[2,3-c]isoquinolin-5-amine


Mass: 183.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 0,1M NaCit, pH 5.9 2,1 M AmmSO4 0,1M Na/K tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.95→42.15 Å / Num. obs: 19398 / % possible obs: 95.5 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-26.70.618781311590.9060.2530.6693.479.2
8.94-42.126.50.03114872290.9990.0130.03347.598.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.9data scaling
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T29

6t29


Resolution: 1.95→42.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.379 / SU ML: 0.096 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 971 5 %RANDOM
Rwork0.1664 ---
obs0.1681 18426 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.57 Å2 / Biso mean: 29.298 Å2 / Biso min: 14.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å2-0 Å2-0.94 Å2
2--1.57 Å2-0 Å2
3----2 Å2
Refinement stepCycle: final / Resolution: 1.95→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2172 0 73 120 2365
Biso mean--42.83 38.64 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122289
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162058
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.6393096
X-RAY DIFFRACTIONr_angle_other_deg0.4881.5744778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.63558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73710371
X-RAY DIFFRACTIONr_chiral_restr0.0670.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 56 -
Rwork0.22 1153 -
all-1209 -
obs--79.23 %

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