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- PDB-6qf4: X-Ray structure of human Serine/Threonine Kinase 17B (STK17B) aka... -

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Basic information

Entry
Database: PDB / ID: 6qf4
TitleX-Ray structure of human Serine/Threonine Kinase 17B (STK17B) aka DRAK2 in complex with ADP obtained by on-chip soaking
ComponentsSerine/threonine-protein kinase 17B
KeywordsTRANSFERASE / STK17B / DRAK2 / ADP / on-chip ligand soaking
Function / homology
Function and homology information


positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process ...positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
Serine/threonine-protein kinase 17B, catalytic domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...Serine/threonine-protein kinase 17B, catalytic domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein kinase 17B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsLieske, J. / Cerv, M. / Kreida, S. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. ...Lieske, J. / Cerv, M. / Kreida, S. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. / Burkhardt, A. / Lane, T.J. / Guenther, S. / Bergtholdt, J. / Schoen, S. / Tornroth-Horsefield, S. / Chapman, H.N. / Meents, A.
Funding support Germany, Sweden, United States, 6items
OrganizationGrant numberCountry
European Research Council609920 Germany
European UnionHorizon 2020, No. 654220 Germany
German Federal Ministry for Education and Research05K2018-2017-06727MXD Germany
Swedish Research Council2010-5208 Sweden
Swedish Research Council2012-2849 Sweden
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Iucrj / Year: 2019
Title: On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies.
Authors: Lieske, J. / Cerv, M. / Kreida, S. / Komadina, D. / Fischer, J. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. ...Authors: Lieske, J. / Cerv, M. / Kreida, S. / Komadina, D. / Fischer, J. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. / Burkhardt, A. / Lane, T.J. / Guenther, S. / Bergtholdt, J. / Schoen, S. / Tornroth-Horsefield, S. / Chapman, H.N. / Meents, A.
History
DepositionJan 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 17B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9356
Polymers37,3271
Non-polymers6085
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-22 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.479, 85.479, 118.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein kinase 17B / DAP kinase-related apoptosis-inducing protein kinase 2


Mass: 37327.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK17B, DRAK2 / Production host: Escherichia coli (E. coli)
References: UniProt: O94768, non-specific serine/threonine protein kinase

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Non-polymers , 6 types, 127 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 7.5
Details: 0.2M ammonium acetate, 20% PEG 3350, 50mM sodium/potassium tartrate, 0.8mM quercetin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.495→42.74 Å / Num. obs: 15529 / % possible obs: 98.6 % / Redundancy: 9.3 % / Biso Wilson estimate: 41.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.036 / Rrim(I) all: 0.113 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.69.70.4935.317430.9220.1660.52299.6
9-42.748.30.0633790.9970.0220.06795.3
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: cryo stream / Sample holding: single crystalline silicon chip / Support base: goniometer

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_9999refinement
Coot0.8.2model building
PHASERphasing
PDB_EXTRACT3.24data extraction
Aimless0.5.8data scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LM5

3lm5


Resolution: 2.495→42.739 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.48
RfactorNum. reflection% reflection
Rfree0.2268 1552 10 %
Rwork0.1827 --
obs0.1871 15521 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.91 Å2 / Biso mean: 57.04 Å2 / Biso min: 16.99 Å2
Refinement stepCycle: final / Resolution: 2.495→42.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 58 122 2487
Biso mean--48.36 51.1 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022425
X-RAY DIFFRACTIONf_angle_d0.4763299
X-RAY DIFFRACTIONf_chiral_restr0.043371
X-RAY DIFFRACTIONf_plane_restr0.002422
X-RAY DIFFRACTIONf_dihedral_angle_d11.7721455
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4953-2.57580.25941390.23861256139599
2.5758-2.66790.30521410.24121258139999
2.6679-2.77470.29491380.22921258139699
2.7747-2.90090.32361370.22741234137198
2.9009-3.05380.25761410.21031263140498
3.0538-3.24510.27561410.2071262140399
3.2451-3.49560.26191380.20031252139098
3.4956-3.84710.25171430.17611278142198
3.8471-4.40330.19571400.14411267140797
4.4033-5.54580.1481420.14151282142497
5.5458-42.74570.20071520.17891359151195
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)
14.57064.729-4.36446.1806-2.45937.4493-0.01620.0105-0.8539-0.4872-0.1668-0.40490.68620.59440.24470.3370.0916-0.10230.43-0.06790.44136.204273.7811-2.2013
24.76742.2543-0.4295.191-0.20653.5879-0.30970.38830.2655-0.25190.2839-0.05460.0044-0.21760.04850.25240.0423-0.03290.2711-0.03380.307929.491684.4754-2.1836
33.622-3.6124-3.29886.06652.82523.8034-0.0895-0.17260.1020.51620.2995-0.3580.30780.1701-0.21070.2741-0.012-0.04350.3246-0.01330.294933.198984.45414.1156
40.02590.25280.17425.709-1.75065.81030.2389-0.2587-0.2156-0.4419-0.08681.9236-0.094-0.99840.07210.2397-0.0030.04240.6173-0.16490.741510.821193.51088.5197
55.08990.0207-2.67054.06510.04056.1035-0.006-0.1616-0.0530.1321-0.0059-0.15590.34930.06650.05510.19020.0596-0.0410.1939-0.0480.334622.818198.582312.0501
68.90191.4175-1.3735.3626-1.72377.6260.34930.64340.1462-0.71340.2687-0.3071-1.03961.0438-0.79030.667-0.01720.17740.5299-0.13240.381331.1998100.9007-0.0247
75.0582-0.13923.4327.2574-3.22838.2449-0.32650.99160.4178-0.83290.07530.048-0.47680.68680.1940.4635-0.0260.09190.5254-0.020.374725.8888110.4675-3.9849
82.88161.088-0.76462.3577-0.37544.30450.16080.21150.3723-0.15760.10850.1732-0.391-0.2832-0.25880.2930.09020.02550.3045-0.03050.396714.7782112.59754.3029
92.5203-0.9347-1.02582.9942-0.44672.4944-0.0788-0.9124-0.0490.6136-0.0598-0.10040.00540.57950.040.4517-0.0198-0.00480.5817-0.0230.481619.8659107.078230.5945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 34 )A18 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 86 )A35 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 110 )A87 - 110
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 131 )A111 - 131
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 174 )A132 - 174
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 196 )A175 - 196
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 214 )A197 - 214
8X-RAY DIFFRACTION8chain 'A' and (resid 215 through 283 )A215 - 283
9X-RAY DIFFRACTION9chain 'A' and (resid 284 through 308 )A284 - 308

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