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

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Basic information

Entry
Database: PDB / ID: 8bfm
TitleCrystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) in complex with FZ331
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 / 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
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
pyrazolo[5,1-a]phthalazin-6-amine / Calcium/calmodulin-dependent protein kinase type 1D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #2)
Authors: Kraemer, A. / Doelle, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionOct 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 2.0May 24, 2023Group: Non-polymer description / Category: chem_comp / Item: _chem_comp.formula
Revision 2.1Feb 7, 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)43,8228
Polymers42,9731
Non-polymers8497
Water2,036113
1
A: Calcium/calmodulin-dependent protein kinase type 1D
hetero molecules

A: Calcium/calmodulin-dependent protein kinase type 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,64316
Polymers85,9462
Non-polymers1,69714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3280 Å2
ΔGint-156 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.531, 44.800, 108.589
Angle α, β, γ (deg.)90.000, 104.260, 90.000
Int Tables number5
Space group name H-MI121

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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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-QI6 / pyrazolo[5,1-a]phthalazin-6-amine


Mass: 184.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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 / Details: 0,1M NaCit, pH 5.9 2,05M AmmSO4 0,1M Na/K tartrate / PH range: 5.9

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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: 1.7→44.95 Å / Num. obs: 28529 / % possible obs: 96.3 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.015 / Rrim(I) all: 0.04 / Net I/σ(I): 21.5
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
1.7-1.737.20.7781079115070.8990.3110.8392.596.5
9-44.96.50.02414292190.9990.010.02660.498.2

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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: 1.7→44.95 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.937 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 1427 5 %RANDOM
Rwork0.2 ---
obs0.2012 27070 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.73 Å2 / Biso mean: 39.411 Å2 / Biso min: 22.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0.24 Å2
2--2.25 Å20 Å2
3----1.69 Å2
Refinement stepCycle: final / Resolution: 1.7→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 53 113 2214
Biso mean--56.94 45.15 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122144
X-RAY DIFFRACTIONr_bond_other_d0.0070.0161898
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.642914
X-RAY DIFFRACTIONr_angle_other_deg0.4371.5764382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.80258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20310331
X-RAY DIFFRACTIONr_chiral_restr0.0610.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 103 -
Rwork0.293 1989 -
all-2092 -
obs--95.92 %
Refinement TLS params.Method: refined / Origin x: -15.1217 Å / Origin y: -21.8305 Å / Origin z: -7.1312 Å
111213212223313233
T0.0868 Å2-0.0598 Å20.0382 Å2-0.1263 Å2-0.0331 Å2--0.0188 Å2
L1.3217 °20.164 °20.6401 °2-0.8501 °21.2769 °2--3.7453 °2
S0.0496 Å °-0.2685 Å °0.0682 Å °0.2402 Å °-0.1856 Å °0.1129 Å °0.2479 Å °-0.5143 Å °0.136 Å °

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