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- PDB-2xik: Structure of Human YSK1 (Yeast Sps1-Ste20-related Kinase 1) -

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Basic information

Entry
Database: PDB / ID: 2xik
TitleStructure of Human YSK1 (Yeast Sps1-Ste20-related Kinase 1)
ComponentsSERINE/THREONINE PROTEIN KINASE 25Serine/threonine-specific protein kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


intrinsic apoptotic signaling pathway in response to hydrogen peroxide / Golgi localization / Golgi reassembly / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / establishment or maintenance of cell polarity / positive regulation of axonogenesis / axonogenesis / response to hydrogen peroxide / response to oxidative stress ...intrinsic apoptotic signaling pathway in response to hydrogen peroxide / Golgi localization / Golgi reassembly / positive regulation of stress-activated MAPK cascade / establishment of Golgi localization / establishment or maintenance of cell polarity / positive regulation of axonogenesis / axonogenesis / response to hydrogen peroxide / response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / signal transduction / protein homodimerization activity / extracellular exosome / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Serine/threonine kinase 25, catalytic domain / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation 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 ...Serine/threonine kinase 25, catalytic domain / Programmed cell death protein 10, dimerisation domain superfamily / : / Programmed cell death protein 10, dimerisation 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
Chem-J60 / Serine/threonine-protein kinase 25
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMuniz, J.R.C. / Rellos, P. / Ugochukwu, E. / Vollmar, M. / Allerston, C. / Chaikuad, A. / Savitsky, P. / Berridge, G. / Brenner, B. / Elkins, J.M. ...Muniz, J.R.C. / Rellos, P. / Ugochukwu, E. / Vollmar, M. / Allerston, C. / Chaikuad, A. / Savitsky, P. / Berridge, G. / Brenner, B. / Elkins, J.M. / Daga, N. / Gileadi, O. / Mahajan, P. / Shrestha, B. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S.
CitationJournal: To be Published
Title: Structure of Human Ysk1 (Yeast Sps1-Ste20-Related Kinase 1)
Authors: Muniz, J.R.C. / Rellos, P. / Vollmar, M. / Allerston, C. / Chaikuad, A. / Savitsky, P. / Berridge, G. / Brenner, B. / Elkins, J.M. / Daga, N. / Gileadi, O. / Mahajan, P. / Shrestha, B. / von ...Authors: Muniz, J.R.C. / Rellos, P. / Vollmar, M. / Allerston, C. / Chaikuad, A. / Savitsky, P. / Berridge, G. / Brenner, B. / Elkins, J.M. / Daga, N. / Gileadi, O. / Mahajan, P. / Shrestha, B. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S.
History
DepositionJun 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Source and taxonomy ...Database references / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE/THREONINE PROTEIN KINASE 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1943
Polymers33,7171
Non-polymers4772
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.080, 48.560, 67.570
Angle α, β, γ (deg.)90.00, 113.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SERINE/THREONINE PROTEIN KINASE 25 / Serine/threonine-specific protein kinase / STERILE 20/OXIDANT STRESS-RESPONSE KINASE 1 / STE20/OXIDANT STRESS RESPONSE KINASE 1 / SOK-1 / ...STERILE 20/OXIDANT STRESS-RESPONSE KINASE 1 / STE20/OXIDANT STRESS RESPONSE KINASE 1 / SOK-1 / STE20-LIKE KINASE


Mass: 33716.566 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: O00506, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-J60 / 5-[(E)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-[2-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE


Mass: 414.928 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27ClN4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.56 Å3/Da / Density % sol: 51.9 % / Description: NONE
Crystal growDetails: 0.2M K3(CIT),0.1M BTPROP 8.5, 20% PEG3350,10% ETGLY

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.97→52.23 Å / Num. obs: 23929 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 32.51 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.8
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER-TNT2.7.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→22.34 Å / Cor.coef. Fo:Fc: 0.9486 / Cor.coef. Fo:Fc free: 0.9275 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=TPO XIK. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2436. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=39. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=TPO XIK. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2436. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=39. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1223 5.1 %RANDOM
Rwork0.1884 ---
obs0.1907 23907 99.5 %-
Displacement parametersBiso mean: 40.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.7682 Å20 Å21.2095 Å2
2---0.3796 Å20 Å2
3---1.1478 Å2
Refine analyzeLuzzati coordinate error obs: 0.263 Å
Refinement stepCycle: LAST / Resolution: 1.97→22.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 33 148 2456
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012390HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.083246HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d805SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes344HARMONIC5
X-RAY DIFFRACTIONt_it2352HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion16.44
X-RAY DIFFRACTIONt_improper_torsion2HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion312SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2750SEMIHARMONIC4
LS refinement shellResolution: 1.97→2.06 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.271 147 5.32 %
Rwork0.2058 2618 -
all0.2093 2765 -
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodOrigin x (Å)Origin y (Å)Origin z (Å)L11 (°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)
1refined3.8022-14.4318-17.364
2refined-6.0622-21.6503-8.67475.9280.12641.20815.4541-3.03112.2395-0.12770.17290.2252-0.18760.0162-0.4582-0.04410.14610.1115-0.15140.0565-0.0444-0.0720.10920.0482
3refined2.2665-19.8296-16.11825.9505-1.1736-0.65940.0757-0.9114-0.4074-0.0982-0.2983-0.1289-0.11070.0873-0.54510.26080.18280.0109-0.04230.0799-0.0811-0.0885-0.03530.0263
4refined-16.4954-14.4993-14.91233.065-1.8203-1.44670-0.3207-1.63940.0429-0.0619-0.09150.2346-0.1564-0.3834-0.06060.39420.11350.00620.0431-0.03970.05360.05170.1373
5refined-23.9239-6.5263-6.5721.68770.4771-0.29152.14140.23042.85170.03670.1509-0.1318-0.02230.061-0.11360.090.0863-0.0977-0.07980.00130.0053-0.0704-0.023-0.0677
6refined-17.1304-6.9687-30.50251.41630.4807-0.12192.33090.26712.28290.0923-0.00210.1840.11150.02390.0975-0.1329-0.1846-0.1162-0.10270.02820.0256-0.08080.0139-0.0343
72.2558-0.7714-0.8524.314-1.37452.53690.22260.4145-0.1424-0.371-0.28520.2208-0.1242-0.02450.06250.05680.02210.00160.09470.0488-0.1324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A23 - A56)
2X-RAY DIFFRACTION2(A57 - A79)
3X-RAY DIFFRACTION3(A80 - A101)
4X-RAY DIFFRACTION4(A102 - A171)
5X-RAY DIFFRACTION5(A172 - A271)
6X-RAY DIFFRACTION6(A272 - A292)

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