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- PDB-5dbx: Crystal structure of murine SPAK(T243D) in complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 5dbx
TitleCrystal structure of murine SPAK(T243D) in complex with AMPPNP
ComponentsSTE20/SPS1-related proline-alanine-rich protein kinase
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


negative regulation of creatine transmembrane transporter activity / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / maintenance of lens transparency / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transporter activity / monoatomic ion homeostasis / negative regulation of potassium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of sodium ion transmembrane transporter activity ...negative regulation of creatine transmembrane transporter activity / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / maintenance of lens transparency / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transporter activity / monoatomic ion homeostasis / negative regulation of potassium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of sodium ion transmembrane transporter activity / positive regulation of T cell chemotaxis / cellular hypotonic response / cellular response to potassium ion / macrophage activation / positive regulation of potassium ion transport / cellular response to chemokine / positive regulation of p38MAPK cascade / response to aldosterone / extrinsic component of membrane / response to dietary excess / sodium ion transmembrane transport / peptidyl-threonine phosphorylation / regulation of blood pressure / kinase activity / cell cortex / cell body / regulation of inflammatory response / basolateral plasma membrane / peptidyl-serine phosphorylation / protein autophosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / intracellular signal transduction / inflammatory response / apical plasma membrane / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / signal transduction / nucleoplasm / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / STE20/SPS1-related proline-alanine-rich protein kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJuang, Y.-C.
CitationJournal: Biochemistry / Year: 2015
Title: Domain-Swapping Switch Point in Ste20 Protein Kinase SPAK.
Authors: Taylor, C.A. / Juang, Y.C. / Earnest, S. / Sengupta, S. / Goldsmith, E.J. / Cobb, M.H.
History
DepositionAug 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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
A: STE20/SPS1-related proline-alanine-rich protein kinase
B: STE20/SPS1-related proline-alanine-rich protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5716
Polymers74,5102
Non-polymers1,0614
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-52 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.442, 101.736, 104.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein STE20/SPS1-related proline-alanine-rich protein kinase / Ste-20-related kinase / Serine/threonine-protein kinase 39


Mass: 37254.828 Da / Num. of mol.: 2 / Fragment: UNP residues 63-390 / Mutation: T243D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stk39, Spak / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Z1W9, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Mg(OAc)2, 0.1 M Tris (pH 8.5), 16% PEG3350 (Hampton), 0.01 M Na- (CH3)2AsO2, and 0.01 M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 27322 / % possible obs: 93 % / Redundancy: 11.28 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 31.4
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c30

2c30


Resolution: 2.5→46.329 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 1184 5.01 %
Rwork0.2063 --
obs0.2083 23625 94.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 64 59 4663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064712
X-RAY DIFFRACTIONf_angle_d1.0276370
X-RAY DIFFRACTIONf_dihedral_angle_d17.3311776
X-RAY DIFFRACTIONf_chiral_restr0.038715
X-RAY DIFFRACTIONf_plane_restr0.004789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61380.3757960.30461953X-RAY DIFFRACTION66
2.6138-2.75160.31261390.27612637X-RAY DIFFRACTION90
2.7516-2.92390.3051480.26572875X-RAY DIFFRACTION98
2.9239-3.14960.32281610.24932921X-RAY DIFFRACTION99
3.1496-3.46650.24521490.22692971X-RAY DIFFRACTION100
3.4665-3.96790.2721730.19352947X-RAY DIFFRACTION100
3.9679-4.99820.18361720.16473000X-RAY DIFFRACTION100
4.9982-46.33740.23261460.19833137X-RAY DIFFRACTION99
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)
16.58882.36373.63815.2711.49547.9723-0.0113-0.74340.22880.4195-0.37040.32110.2335-0.68910.31220.373-0.0230.0180.6294-0.16030.4068-11.4096-12.944535.6886
28.46183.71132.44658.810.42237.37440.8340.2033-1.64290.9982-0.4103-0.47541.90870.9724-0.6831.53990.1309-0.10330.7725-0.13761.098-4.4773-30.262531.8828
33.27221.50642.22463.322-1.05773.11990.0997-0.213-0.2510.0739-0.0604-0.66150.19910.65870.02740.3506-0.0027-0.06720.53650.00870.5664-4.8328-17.152425.3856
44.65350.38743.422.34260.13284.40850.117-0.70050.919-0.1456-0.53981.0136-0.3496-0.75010.22590.40370.1535-0.17340.449-0.15870.7891-23.3887-11.12319.732
53.4151-1.31820.86729.2920.70835.7688-0.8050.19850.7488-0.42110.4373-0.9913-0.71810.57840.08720.4992-0.2052-0.00450.4350.05040.4057-10.9685-14.45548.1103
64.4625-1.1364-0.58296.17542.43433.9776-0.4143-0.705-0.1085-0.01640.53960.1409-0.26110.54020.08410.3769-0.0163-0.03750.4652-0.02880.4873-14.169-21.010215.986
70.6218-0.4787-0.19468.21872.5342.7374-0.1207-0.39940.11092.1709-0.0201-0.6080.4170.1746-0.00550.642-0.1083-0.05320.6153-0.00340.5986-11.6319-31.711817.6456
81.0503-0.43710.35577.83541.98832.7775-0.4398-0.44220.13570.31340.6331-0.72440.0640.0830.14840.23480.01170.07550.30490.00470.397-16.425-30.80828.0396
95.42810.3789-0.64655.35021.01934.0311-0.28330.43050.4765-0.778-0.00730.9036-0.5958-0.39080.33580.46710.0656-0.16450.5635-0.07870.459-29.1274-23.25982.1133
103.72481.64870.69695.31710.8282.9983-0.62490.5680.6896-1.6210.5089-0.3436-1.0850.45070.25040.6932-0.163-0.05480.49590.07730.5842-14.9005-12.51723.4999
113.95490.0335-2.66771.1716-0.58466.77360.0337-0.5002-0.03390.1942-0.1267-0.2501-0.0928-0.09320.10970.4654-0.0773-0.03870.44580.13760.5374-19.702-67.945426.1777
120.9458-0.24190.4725.4157-0.67590.37080.1072-0.1287-0.05210.542-0.22010.1475-0.021-0.14980.10950.3789-0.02060.02360.4270.06770.3793-20.1935-56.675411.1636
135.11840.28510.9797.02220.59852.5812-0.05110.6907-0.3335-0.7012-0.0223-0.56280.14830.0470.06040.4842-0.00910.09150.56710.09810.423-11.2748-63.2103-0.0337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 65 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 142 )
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 177 )
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 212 )
7X-RAY DIFFRACTION7chain 'A' and (resid 213 through 252 )
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 280 )
9X-RAY DIFFRACTION9chain 'A' and (resid 281 through 329 )
10X-RAY DIFFRACTION10chain 'A' and (resid 330 through 365 )
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 177 )
12X-RAY DIFFRACTION12chain 'B' and (resid 178 through 280 )
13X-RAY DIFFRACTION13chain 'B' and (resid 281 through 364 )

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