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- PDB-5ig1: Crystal structure of S. rosetta CaMKII kinase domain -

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Basic information

Entry
Database: PDB / ID: 5ig1
TitleCrystal structure of S. rosetta CaMKII kinase domain
ComponentsCAMK/CAMK2 protein kinase
KeywordsTRANSFERASE / Ca2+/CaM-dependent kinase / choanoflagellate
Function / homology
Function and homology information


cellular anatomical entity / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / calmodulin binding / protein phosphorylation / ATP binding
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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 ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / 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
PHOSPHATE ION / calcium/calmodulin-dependent protein kinase
Similarity search - Component
Biological speciesSalpingoeca rosetta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBhattacharyya, M. / Gee, C.L. / Barros, T. / Kuriyan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)NA United States
CitationJournal: Elife / Year: 2016
Title: Molecular mechanism of activation-triggered subunit exchange in Ca(2+)/calmodulin-dependent protein kinase II.
Authors: Bhattacharyya, M. / Stratton, M.M. / Going, C.C. / McSpadden, E.D. / Huang, Y. / Susa, A.C. / Elleman, A. / Cao, Y.M. / Pappireddi, N. / Burkhardt, P. / Gee, C.L. / Barros, T. / Schulman, H. ...Authors: Bhattacharyya, M. / Stratton, M.M. / Going, C.C. / McSpadden, E.D. / Huang, Y. / Susa, A.C. / Elleman, A. / Cao, Y.M. / Pappireddi, N. / Burkhardt, P. / Gee, C.L. / Barros, T. / Schulman, H. / Williams, E.R. / Kuriyan, J.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Structure summary
Revision 1.2Jul 13, 2016Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: CAMK/CAMK2 protein kinase
B: CAMK/CAMK2 protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5855
Polymers78,3002
Non-polymers2853
Water63135
1
A: CAMK/CAMK2 protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3403
Polymers39,1501
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CAMK/CAMK2 protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2452
Polymers39,1501
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.031, 100.031, 123.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsAs per the authors the biological assembly is unknown

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Components

#1: Protein CAMK/CAMK2 protein kinase


Mass: 39150.066 Da / Num. of mol.: 2 / Fragment: UNP residues 1-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salpingoeca rosetta (eukaryote) / Strain: ATCC 50818 / BSB-021 / Gene: PTSG_10090 / Production host: Escherichia coli (E. coli) / References: UniProt: F2UPG5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.98 Å3/Da / Density % sol: 69.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic pH 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2014 / Details: M1: parabola M2: torroid
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→46.58 Å / Num. obs: 27096 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 51.72 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 8.4
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BDW

2bdw


Resolution: 2.9→46.58 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 25.27
RfactorNum. reflection% reflection
Rfree0.2243 1319 4.86 %
Rwork0.1826 --
obs0.1847 25737 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 15 35 4920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045000
X-RAY DIFFRACTIONf_angle_d0.5996765
X-RAY DIFFRACTIONf_dihedral_angle_d12.883025
X-RAY DIFFRACTIONf_chiral_restr0.044737
X-RAY DIFFRACTIONf_plane_restr0.004866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.95590.30191200.31212871X-RAY DIFFRACTION100
2.9559-3.01620.37331220.29092832X-RAY DIFFRACTION100
3.0162-3.08170.36311500.28222782X-RAY DIFFRACTION100
3.0817-3.15340.30991280.26152818X-RAY DIFFRACTION100
3.1534-3.23230.33171600.24252811X-RAY DIFFRACTION100
3.2323-3.31960.29141340.2192826X-RAY DIFFRACTION100
3.3196-3.41730.25361500.21982772X-RAY DIFFRACTION100
3.4173-3.52750.27051460.20232805X-RAY DIFFRACTION100
3.5275-3.65360.22931300.19592823X-RAY DIFFRACTION100
3.6536-3.79980.23641520.18612801X-RAY DIFFRACTION100
3.7998-3.97260.18131220.16342846X-RAY DIFFRACTION100
3.9726-4.1820.19231470.14812815X-RAY DIFFRACTION100
4.182-4.44380.18111250.13642799X-RAY DIFFRACTION100
4.4438-4.78660.15911800.13322779X-RAY DIFFRACTION100
4.7866-5.26770.16571600.14662805X-RAY DIFFRACTION100
5.2677-6.02850.23851340.18392805X-RAY DIFFRACTION100
6.0285-7.590.21211560.18172809X-RAY DIFFRACTION100
7.59-46.58580.23411660.17082785X-RAY DIFFRACTION100
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)
13.9930.86350.49967.00021.29023.3288-0.340.45240.3823-0.90340.0960.4985-0.2143-0.28560.12740.46860.0257-0.11250.33150.03590.3903-15.937128.4421-15.1608
24.32770.22481.96280.9039-0.42832.8634-0.2674-0.20770.5257-0.08570.02210.0923-0.3056-0.1680.26520.35480.08040.01590.3062-0.030.279-10.345623.65220.5744
36.5940.52541.12682.3028-0.41712.01310.0961-0.9218-1.00060.1474-0.01630.02040.2037-0.3184-0.05760.330.08160.04840.51390.090.3293-7.561510.088311.6921
42.01244.7796.54268.23492.06079.26660.46021.0313-0.2923-0.79530.1033-0.73620.64380.0123-0.67740.50550.13060.11910.5885-0.08610.37475.28159.2179-1.6109
55.5929-1.95081.33122.02160.86725.2353-0.13170.7979-0.803-0.1933-0.27260.90770.0403-0.61780.32630.52020.02450.09630.87730.02370.7512-40.53919.6215-1.3748
62.83890.976-2.69141.5329-0.5652.625-0.3654-0.1711-1.1323-0.0014-0.1052-0.4210.3615-0.06030.37830.37790.03460.01520.82340.19010.9011-40.45324.26613.7734
76.50791.2787-0.1731.7801-1.54011.7058-0.4314-0.8736-1.75090.06770.0363-0.21370.0656-0.00810.3510.4234-0.02530.12620.74780.29910.7747-54.96170.9822.4106
81.8887-1.85280.52022.00690.45024.5231-0.4306-0.7888-2.2712-0.0434-0.6001-0.46121.7862-0.0117-0.09780.75430.18950.29941.08730.96372.1985-48.7115-13.424828.161
93.4932-4.0066-0.57456.40890.44752.9007-0.2661-1.1781-1.5790.2020.0114-0.99820.67180.59440.0930.7480.14590.30021.27110.6412.0199-36.4785-11.872426.1004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 286 )
4X-RAY DIFFRACTION4chain 'A' and (resid 287 through 302 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 156 )
7X-RAY DIFFRACTION7chain 'B' and (resid 157 through 195 )
8X-RAY DIFFRACTION8chain 'B' and (resid 196 through 265 )
9X-RAY DIFFRACTION9chain 'B' and (resid 266 through 302 )

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