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- PDB-7q7e: Room temperature structure of the human Serine/Threonine Kinase 1... -

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Basic information

Entry
Database: PDB / ID: 7q7e
TitleRoom temperature structure of the human Serine/Threonine Kinase 17B (STK17B/DRAK2) in complex with ATP/ADP at atmospheric pressure in a sapphire capillary after high helium gas pressure release
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'-TRIPHOSPHATE / 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: Fixed-target high-pressure macromolecular crystallography
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,8593
Polymers37,3271
Non-polymers5312
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-14 kcal/mol
Surface area13380 Å2
Unit cell
Length a, b, c (Å)84.240, 84.240, 117.260
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
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/50 mM magnesium chloride in DRAK2 crystallization buffer and incubated for half an hour.
PH range: 6.5-7.5 / Pressure: 101.325 kPa

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Data collection

DiffractionAmbient environment: gaseous He / Ambient pressure: 101.325 kPa / Mean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.477 Å
DetectorType: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Sep 30, 2019
Diffraction measurementSpecimen support: sapphire capillary
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.477 Å / Relative weight: 1
ReflectionResolution: 2.85→48.12 Å / Num. obs: 9542 / % possible obs: 91.75 % / Redundancy: 20.8 % / Biso Wilson estimate: 69.36 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.35 / Rpim(I) all: 0.076 / Rrim(I) all: 0.359 / Net I/σ(I): 9.44
Reflection shellResolution: 2.85→2.952 Å / Redundancy: 21.1 % / Rmerge(I) obs: 3.753 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 930 / CC1/2: 0.336 / CC star: 0.709 / Rpim(I) all: 0.812 / Rrim(I) all: 3.845 / % possible all: 92.9
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→48.12 Å / SU ML: 0.3854 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5237 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2392 955 10.02 %
Rwork0.1856 8579 -
obs0.191 9534 91.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.23 Å2
Refinement stepCycle: LAST / Resolution: 2.85→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 32 11 2295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272359
X-RAY DIFFRACTIONf_angle_d0.56583211
X-RAY DIFFRACTIONf_chiral_restr0.0427362
X-RAY DIFFRACTIONf_plane_restr0.0027401
X-RAY DIFFRACTIONf_dihedral_angle_d12.68811395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-30.33411350.29941207X-RAY DIFFRACTION92.87
3-3.190.34731320.2791193X-RAY DIFFRACTION92.92
3.19-3.430.34181340.25291214X-RAY DIFFRACTION92.58
3.43-3.780.25941360.19171220X-RAY DIFFRACTION92.18
3.78-4.330.20951360.15311215X-RAY DIFFRACTION91.9
4.33-5.450.17931360.14631231X-RAY DIFFRACTION91.01
5.45-48.120.22051460.16981299X-RAY DIFFRACTION89.42
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)
14.03005840803-0.1702148966280.09150679132455.457685499522.039452051144.83576670174-0.205750192130.159825714833-0.162422604570.1474168676660.1338188143270.05694627772670.256842408459-0.2275121029889.43595863596E-50.466091709751-0.0112236849253-0.07057167566940.47010801046-0.005109535845460.52668981528331.337303533580.8884609083-0.600904199571
20.2424837671950.284798176428-0.1940769703640.455938819055-0.02819578174570.472960689051-0.0952289554582-0.206423079895-0.518641372693-0.2478203967-0.1363029407971.63991865053-0.158856004627-1.05476428578-0.001118802999930.535180070509-0.0207272708711-0.01059388177560.999851383125-0.125376110090.91068376024510.019750948292.58278493758.36144197316
34.00305525428-0.4983411742652.300521562264.941539672441.420651245542.944369672460.0543439774340.578376859916-0.0372955505127-0.375270988239-0.0553519961641-0.0982885133248-0.1907917250880.463327056491-0.000124156128690.5819553993330.00455510942021-0.002095727012080.616964824107-0.0891075635990.61177856285625.3632003926100.0391400864.75089966229
44.447094263650.68257735029-1.842079191833.461683703941.226678648482.19178611735-0.07933334468920.6132388628850.448818056626-0.2631155999780.118416655005-0.0948109653381-0.515689620916-0.3088986480955.16004037755E-50.5611062846970.09146651139110.03252358262610.686252393763-0.01113115335420.61858275199216.1166291349109.9386944847.41176775783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 111 )
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 131 )
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 301 )

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