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- PDB-4ynz: Structure of the N-terminal domain of SAD -

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Basic information

Entry
Database: PDB / ID: 4ynz
TitleStructure of the N-terminal domain of SAD
ComponentsSerine/threonine-protein kinase BRSK2
KeywordsTRANSFERASE / kinase domain / UBA 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 / establishment of cell polarity / regulation of axonogenesis / 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 / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity / exocytosis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / ERAD pathway / 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 Å
AuthorsWu, J.X. / Wang, J. / Chen, L. / Wang, Z.X. / Wu, J.W.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31130062 China
National Natural Science Foundation of China31321003 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 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 1.2Nov 8, 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: Serine/threonine-protein kinase BRSK2
B: Serine/threonine-protein kinase BRSK2


Theoretical massNumber of molelcules
Total (without water)78,8262
Polymers78,8262
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-3 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.299, 60.745, 73.937
Angle α, β, γ (deg.)103.74, 106.48, 107.42
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 39412.773 Da / Num. of mol.: 2 / Fragment: UNP residues 15-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brsk2 / Plasmid: PGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q69Z98, tau-protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris, 15% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 16, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 42329 / % possible obs: 96.2 % / Redundancy: 2.3 % / Biso Wilson estimate: 35.58 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.3 / % possible all: 85.7

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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: 2HAK

2hak


Resolution: 2→29.675 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2124 5.06 %Random selection
Rwork0.19 ---
obs0.192 41937 96.27 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.969 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 48.61 Å2
Baniso -1Baniso -2Baniso -3
1-3.4231 Å2-0.2844 Å2-1.7464 Å2
2---3.3674 Å2-3.0782 Å2
3----0.0381 Å2
Refinement stepCycle: LAST / Resolution: 2→29.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5153 0 0 163 5316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085257
X-RAY DIFFRACTIONf_angle_d1.117076
X-RAY DIFFRACTIONf_dihedral_angle_d14.962039
X-RAY DIFFRACTIONf_chiral_restr0.075784
X-RAY DIFFRACTIONf_plane_restr0.004903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.29891380.26172387X-RAY DIFFRACTION87
2.0465-2.09770.3331460.24162530X-RAY DIFFRACTION91
2.0977-2.15440.2771490.23772531X-RAY DIFFRACTION93
2.1544-2.21780.28681430.21722607X-RAY DIFFRACTION95
2.2178-2.28930.26041570.20022652X-RAY DIFFRACTION97
2.2893-2.37110.25911330.20222720X-RAY DIFFRACTION97
2.3711-2.4660.23451310.22708X-RAY DIFFRACTION98
2.466-2.57820.27081370.20332695X-RAY DIFFRACTION98
2.5782-2.7140.27151440.19392712X-RAY DIFFRACTION98
2.714-2.88390.25171380.19632729X-RAY DIFFRACTION98
2.8839-3.10640.24851370.19422716X-RAY DIFFRACTION98
3.1064-3.41860.22551440.18772698X-RAY DIFFRACTION99
3.4186-3.91230.19511420.17212764X-RAY DIFFRACTION99
3.9123-4.92540.18191420.15732716X-RAY DIFFRACTION99
4.9254-29.67780.22071430.20172648X-RAY DIFFRACTION96
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)
11.8173-0.85320.15462.1983-0.35162.1606-0.2696-0.29380.11910.5510.1399-0.0476-0.4593-0.20220.07440.40240.0609-0.01910.36260.02060.4216-32.509727.892250.3561
22.1470.0404-0.7441.9541-0.44632.5538-0.2105-0.47440.3480.3552-0.0468-0.2022-0.6991-0.01180.12490.36780.0115-0.09630.3360.01910.2587-23.904733.032842.6297
31.0534-0.5471-0.61221.1262-0.77532.3690.0382-0.01760.04220.2352-0.0652-0.11710.0228-0.53830.05390.2325-0.0521-0.01170.330.0430.2623-29.861422.791336.8417
41.4814-0.3366-0.45112.1142-0.74352.8884-0.0899-0.00480.01180.0456-0.0157-0.18370.077-0.01430.01320.1508-0.05020.03360.27690.01760.2453-20.582418.639828.7125
52.68680.40830.15352.16820.16182.6195-0.01360.0647-0.7495-0.2290.0274-0.39070.84640.2759-0.0390.4010.09350.07390.33960.00630.4588-12.23655.035325.6502
63.4555-0.23681.56811.7756-0.03832.3398-0.14950.60310.3759-0.4628-0.0795-0.28530.10710.46740.0930.3177-0.05760.09060.41690.00270.267-15.607117.588716.031
71.04380.4034-0.03072.56751.0191.53810.10090.4570.4247-0.02660.10570.432-0.6279-0.2531-0.1080.6270.04140.020.24530.00520.2934-20.394847.120726.8784
83.82450.38630.89722.8541-0.19622.90560.2441-0.2134-0.23110.31630.032-0.0631-0.10420.0663-0.15220.4263-0.0243-0.05930.2254-0.00480.1859-16.154544.379330.346
90.81390.1396-0.22312.9382-0.24143.1242-0.18660.1678-0.019-0.28180.23340.00310.4214-0.0689-0.0280.2073-0.0396-0.00990.1947-0.00730.1555-30.21195.954855.9697
102.6509-0.4338-0.23692.272-0.03552.1012-0.1354-0.24080.29930.30450.1218-0.3936-0.16720.42940.02170.31810.0348-0.11350.2847-0.05870.3431-19.442818.561771.2993
112.0251-1.40820.2932.88430.47550.5861-0.0081-0.1091-0.34130.21460.19640.19540.20890.032-0.14730.66170.1342-0.05780.33630.01660.3938-26.4905-11.531969.2921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 9:39)
2X-RAY DIFFRACTION2chain 'A' and (resseq 40:73)
3X-RAY DIFFRACTION3chain 'A' and (resseq 74:115)
4X-RAY DIFFRACTION4chain 'A' and (resseq 116:212)
5X-RAY DIFFRACTION5chain 'A' and (resseq 213:251)
6X-RAY DIFFRACTION6chain 'A' and (resseq 252:272)
7X-RAY DIFFRACTION7chain 'A' and (resseq 273:310)
8X-RAY DIFFRACTION8chain 'A' and (resseq 311:343)
9X-RAY DIFFRACTION9chain 'B' and (resseq 9:158)
10X-RAY DIFFRACTION10chain 'B' and (resseq 159:274)
11X-RAY DIFFRACTION11chain 'B' and (resseq 275:343)

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