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- PDB-4yom: Structure of SAD kinase -

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Basic information

Entry
Database: PDB / ID: 4yom
TitleStructure of SAD kinase
Components(Serine/threonine-protein kinase BRSK2) x 2
KeywordsTRANSFERASE / kinase domain / UBA domain / KA1 domain
Function / homology
Function and homology information


distal axon / microtubule cytoskeleton organization involved in establishment of planar polarity / : / regulation of insulin secretion involved in cellular response to glucose stimulus / tau-protein kinase / regulation of neuron projection development / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / exocytosis ...distal axon / microtubule cytoskeleton organization involved in establishment of planar polarity / : / regulation of insulin secretion involved in cellular response to glucose stimulus / tau-protein kinase / regulation of neuron projection development / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / exocytosis / ERAD pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / axonogenesis / neuron projection morphogenesis / neuron differentiation / G2/M transition of mitotic cell cycle / ATPase binding / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein kinase binding / perinuclear region of cytoplasm / magnesium ion binding / endoplasmic reticulum / ATP binding / 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
Serine/threonine-protein kinase BRSK2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsWu, J.X. / Wang, J. / Chen, L. / Wang, Z.X. / Wu, J.W.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation31130062 China
National Natural Science Foundation31321003 China
Ministry of Science and Technology2011CB910800 China
Ministry of Science and Technology2013CB530600 China
CitationJournal: Nat Commun / Year: 2015
Title: Structural insight into the mechanism of synergistic autoinhibition of SAD kinases
Authors: Wu, J.X. / Cheng, Y.S. / Wang, J. / Chen, L. / Ding, M. / Wu, J.W.
History
DepositionMar 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Serine/threonine-protein kinase BRSK2
A: Serine/threonine-protein kinase BRSK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5114
Polymers56,3872
Non-polymers1242
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-8 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.111, 87.271, 80.301
Angle α, β, γ (deg.)90.00, 92.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serine/threonine-protein kinase BRSK2 / SADa / Serine/threonine-protein kinase SAD-A


Mass: 40171.516 Da / Num. of mol.: 1 / Fragment: UNP residues 1-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brsk2 / Plasmid: PET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q69Z98, tau-protein kinase
#2: Protein Serine/threonine-protein kinase BRSK2 / SADa / Serine/threonine-protein kinase SAD-A


Mass: 16215.451 Da / Num. of mol.: 1 / Fragment: UNP residues 519-653
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brsk2 / Plasmid: PET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q69Z98, tau-protein kinase
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence of chain A is Isoform 4 SADA-alpha.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 0.1 M Na Citrate, 1.0 M Na Malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 23808 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 56.79 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 26.9
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OSE

3ose


Resolution: 2.49→34.579 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1217 5.13 %Random selection
Rwork0.1966 ---
obs0.1986 23731 99.73 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.315 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 54.27 Å2
Baniso -1Baniso -2Baniso -3
1-40.7059 Å20 Å25.3937 Å2
2--17.5427 Å2-0 Å2
3---2.6899 Å2
Refinement stepCycle: LAST / Resolution: 2.49→34.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 8 67 3515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083512
X-RAY DIFFRACTIONf_angle_d1.0854722
X-RAY DIFFRACTIONf_dihedral_angle_d16.761337
X-RAY DIFFRACTIONf_chiral_restr0.075531
X-RAY DIFFRACTIONf_plane_restr0.004596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4902-2.58990.26631380.25112446X-RAY DIFFRACTION98
2.5899-2.70770.32461470.25662469X-RAY DIFFRACTION100
2.7077-2.85040.32071290.232514X-RAY DIFFRACTION100
2.8504-3.02890.26081300.23272472X-RAY DIFFRACTION100
3.0289-3.26260.23621250.22082531X-RAY DIFFRACTION100
3.2626-3.59060.25491420.20422480X-RAY DIFFRACTION100
3.5906-4.10950.22261170.18092546X-RAY DIFFRACTION100
4.1095-5.17470.19471400.16612512X-RAY DIFFRACTION100
5.1747-34.58180.23521490.19232544X-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)
17.0946-2.92991.64578.3938-3.32286.97950.166-0.45210.13740.5878-0.1167-1.05340.17080.92590.07270.4116-0.0046-0.09580.46070.05650.2966-5.734326.9438-11.1251
21.74251.2790.02062.9373-2.38042.17180.13250.01990.10330.2274-0.0936-0.0337-0.11750.0533-0.06650.17720.06340.02680.1873-0.07980.176-16.773615.1799-6.3971
35.5518-1.5466-2.21661.0837-0.51292.96180.01610.7562-0.079-0.39010.0332-0.4879-0.26360.09290.11320.4632-0.00560.110.296-0.0220.4053-6.80240.4927-5.3905
46.26390.26630.25612.84-0.26163.75660.079-0.6254-0.43360.1205-0.14070.07180.4112-0.18120.05950.3105-0.07920.04850.2395-0.01660.2193-18.0698-2.53667.9758
51.8905-0.3501-1.54271.17310.59065.7301-0.11440.4823-0.1851-0.3799-0.16230.2760.0235-0.67380.3020.5612-0.0256-0.04820.6213-0.12630.3891-30.28658.7522-24.6366
66.6399-1.9654-0.0728.26253.77452.21160.49070.6879-0.88960.1046-0.4190.49040.6157-0.82290.0670.5483-0.0931-0.01210.6386-0.17260.2305-29.42996.5205-25.5722
70.9172-20.88865.2131-0.69422.10020.25270.41630.0128-0.3069-0.19580.1732-0.14910.2797-0.07620.4524-0.00490.05160.53550.09630.3344-17.392934.4108-29.5124
86.46521.35162.81078.6164-0.54156.62680.55190.1804-0.2161-0.5566-0.3120.18730.51250.0584-0.31790.54060.08670.02290.3676-0.0040.2506-20.626936.681-30.2725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 13:32)
2X-RAY DIFFRACTION2chain 'B' and (resseq 33:166)
3X-RAY DIFFRACTION3chain 'B' and (resseq 167:194)
4X-RAY DIFFRACTION4chain 'B' and (resseq 195:272)
5X-RAY DIFFRACTION5chain 'B' and (resseq 273:315)
6X-RAY DIFFRACTION6chain 'B' and (resseq 316:344)
7X-RAY DIFFRACTION7chain 'A' and (resseq 519:565)
8X-RAY DIFFRACTION8chain 'A' and (resseq 566:636)

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