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- PDB-7q7c: Room temperature structure of the human Serine/Threonine Kinase 1... -

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Basic information

Entry
Database: PDB / ID: 7q7c
TitleRoom temperature structure of the human Serine/Threonine Kinase 17B (STK17B/DRAK2) in complex with ADP at atmospheric pressure
ComponentsSerine/threonine-protein kinase 17B
KeywordsTRANSFERASE / HPMX / high-pressure macromolecular crystallography / sapphire capillary / room temperature
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 / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein kinase 17B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLieske, J. / Guenther, S. / Saouane, S. / Meents, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B0405A Germany
CitationJournal: To Be Published
Title: Room temperature structure of the human Serine/Threonine Kinase 17B (STK17B/DRAK2) in complex with ADP at atmospheric pressure
Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / ...Authors: Lieske, J. / Saouane, S. / Guenther, S. / Meyer, J. / Pakendorf, T. / Reime, B. / Burkhardt, A. / Crosas, E. / Hakanpaeae, J. / Stachnik, K. / Sieg, J. / Rarey, M. / Abdellatif, M.H. / Gabdulkhakov, A.G. / Selikhanov, G.K. / Chapman, H.N. / Meents, A.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,7793
Polymers37,3271
Non-polymers4522
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-16 kcal/mol
Surface area13350 Å2
Unit cell
Length a, b, c (Å)84.440, 84.440, 116.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4

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Components

#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
#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-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 295 K / Method: batch mode
Details: 20 mg/ml protein in 25 mM HEPES pH 7.5, 500 mM NaCl, 0.5 mM TCEP was mixed 1:1.5 with precipitant solution (0.1 M HEPES 6.5, 0.2M ammonium acetate, 20% PEG 3350, 50mM sodium/potassium ...Details: 20 mg/ml protein in 25 mM HEPES pH 7.5, 500 mM NaCl, 0.5 mM TCEP was mixed 1:1.5 with precipitant solution (0.1 M HEPES 6.5, 0.2M ammonium acetate, 20% PEG 3350, 50mM sodium/potassium tartrate, 0.8mM quercetin). Batch grown crystals were subsequently mixed 1:1 with 100 mM ATP/50mM magnesium chloride in DRAK2 crystallization buffer and incubated for half an hour.
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Nov 15, 2019
Diffraction measurementSpecimen support: sapphire capillary
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→47.98 Å / Num. obs: 10282 / % possible obs: 98.91 % / Redundancy: 7.8 % / Biso Wilson estimate: 92.37 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.074 / Rrim(I) all: 0.215 / Net I/σ(I): 5.93
Reflection shellResolution: 2.85→2.952 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.085 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 982 / CC1/2: 0.457 / CC star: 0.792 / Rpim(I) all: 0.486 / Rrim(I) all: 1.195 / % possible all: 97.31
Cell measurementPressure: 101.325 kPa

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Processing

Software
NameVersionClassification
PHENIX1.13-2998_9999refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QF4

6qf4


Resolution: 2.85→47.98 Å / SU ML: 0.4636 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9839 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2376 1027 10 %
Rwork0.2072 9244 -
obs0.2102 10271 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.15 Å2
Refinement stepCycle: LAST / Resolution: 2.85→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 28 6 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232271
X-RAY DIFFRACTIONf_angle_d0.48023086
X-RAY DIFFRACTIONf_chiral_restr0.0419350
X-RAY DIFFRACTIONf_plane_restr0.0027390
X-RAY DIFFRACTIONf_dihedral_angle_d11.90291359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-30.38691410.35751272X-RAY DIFFRACTION97.58
3-3.190.32041410.30341266X-RAY DIFFRACTION98.53
3.19-3.430.33061440.27441298X-RAY DIFFRACTION98.97
3.43-3.780.26141450.23831310X-RAY DIFFRACTION99.39
3.78-4.330.22641460.18341309X-RAY DIFFRACTION99.39
4.33-5.450.18031500.1731352X-RAY DIFFRACTION99.67
5.45-47.980.22911600.18941437X-RAY DIFFRACTION99.07
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)
12.77624995028-1.72253705841-1.659115106295.680584503942.634711144852.97711748595-0.1180934756910.139102856302-0.02407231876050.2601581009480.07281102030830.2340707660080.239673298143-0.1161769735364.23223612584E-50.718058776782-0.0353517642254-0.07074936441470.8285199320560.00328372161650.77642779154326.580382115786.69353857893.88354374891
20.9495726496350.02998612947240.9523677430420.7105578908130.01958660028670.931478443447-0.0207728591810.8858791215870.0862867444819-0.3486284929420.0983881876624-0.90486593497-0.9181253066240.9764927452790.0001329102190131.26736395473-0.08625101719510.1324143362741.10962625463-0.04463531107040.96969028730528.5676368684103.655343756-1.19890105921
34.8312066285-0.0931945054293-1.70820275443.93729681061.660842370612.361712569930.09091660435560.5172514391110.84491244153-0.374872615910.131825106681-0.295347903013-0.766664307377-0.4195485163659.91449731777E-50.864638073530.08548261159580.1081295650630.9170316331390.03363647289690.90332138112616.3968371202109.9923691017.43010710388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 213 )
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 297 )

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