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- PDB-2buj: Crystal structure of the human Serine-threonine Kinase 16 in comp... -

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Basic information

Entry
Database: PDB / ID: 2buj
TitleCrystal structure of the human Serine-threonine Kinase 16 in complex with staurosporine
ComponentsSERINE/THREONINE-PROTEIN KINASE 16
KeywordsTRANSFERASE / ATP-BINDING / KINASE / LIPOPROTEIN / MYRISTATE / PALMITATE / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


Golgi-associated vesicle / cellular response to transforming growth factor beta stimulus / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / protein autophosphorylation / non-specific serine/threonine protein kinase / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein serine kinase activity / protein serine/threonine kinase activity ...Golgi-associated vesicle / cellular response to transforming growth factor beta stimulus / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / protein autophosphorylation / non-specific serine/threonine protein kinase / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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 domain profile. ...: / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
STAUROSPORINE / Serine/threonine-protein kinase 16
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDebreczeni, J.E. / Eswaran, J. / Bullock, A. / Filippakopoulos, P. / Kavanagh, K. / Amos, A. / Fedorov, O. / Sobott, F. / Ball, L.J. / von Delft, F. ...Debreczeni, J.E. / Eswaran, J. / Bullock, A. / Filippakopoulos, P. / Kavanagh, K. / Amos, A. / Fedorov, O. / Sobott, F. / Ball, L.J. / von Delft, F. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of the Human Serine-Threonine Kinase 16 in Complex with Staurosporine
Authors: Debreczeni, J.E. / Eswaran, J. / Bullock, A. / Filippakopoulos, P. / Kavanagh, K. / Amos, A. / Fedorov, O. / Sobott, F. / Ball, L.J. / von Delft, F. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Knapp, S.
History
DepositionJun 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE 16
B: SERINE/THREONINE-PROTEIN KINASE 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5508
Polymers72,6132
Non-polymers1,9376
Water1,36976
1
A: SERINE/THREONINE-PROTEIN KINASE 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2754
Polymers36,3061
Non-polymers9693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERINE/THREONINE-PROTEIN KINASE 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2754
Polymers36,3061
Non-polymers9693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.554, 168.901, 129.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.77547, 0.63133, 0.00832), (0.59873, 0.7311, 0.32714), (0.20045, 0.25867, -0.94494)
Vector: -24.64208, 16.92329, -47.67651)

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE 16 / HUMAN SERINE THREONINE KINASE 16 / PROTEIN KINASE PKL12 / MYRISTOYLATED AND PALMITOYLATED ...HUMAN SERINE THREONINE KINASE 16 / PROTEIN KINASE PKL12 / MYRISTOYLATED AND PALMITOYLATED SERINE/THREONINE KINASE / MPSK / TGF-BETA STIMULATED FACTOR 1 / TSF-1 / HPSK


Mass: 36306.488 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P11-TORONTO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA II / References: UniProt: O75716, EC: 2.7.1.37
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 18 TO HIS ENGINEERED RESIDUE IN CHAIN B, ARG 18 TO HIS ...ENGINEERED RESIDUE IN CHAIN A, ARG 18 TO HIS ENGINEERED RESIDUE IN CHAIN B, ARG 18 TO HIS ENGINEERED RESIDUE IN CHAIN A, ARG 265 TO TRP ENGINEERED RESIDUE IN CHAIN B, ARG 265 TO TRP
Sequence detailsMUTATION R18H AND R265W

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.3 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 200 NL SITTING DROP, 1.1 AMMONIUM SULFATE, 1% PEG3350, 0.1 M BIS-TRIS PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.984
DetectorType: MARRESEARCH / Detector: CCD / Date: May 23, 2005 / Details: MIRRORS
RadiationMonochromator: SILICON MONOCHROMATORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.6→64.8 Å / Num. obs: 35446 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.83 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.52
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5.12 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.29 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→64.82 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.62 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1792 5.1 %RANDOM
Rwork0.185 ---
obs0.187 33626 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2---0.9 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→64.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 142 76 4766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214828
X-RAY DIFFRACTIONr_bond_other_d0.0010.024321
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9926597
X-RAY DIFFRACTIONr_angle_other_deg0.88739961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93123.71221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75115756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8791529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021001
X-RAY DIFFRACTIONr_nbd_refined0.2010.2952
X-RAY DIFFRACTIONr_nbd_other0.1820.24106
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22311
X-RAY DIFFRACTIONr_nbtor_other0.0890.22818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.24432985
X-RAY DIFFRACTIONr_mcbond_other0.44431170
X-RAY DIFFRACTIONr_mcangle_it3.50554575
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.87272863
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.821112022
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.312 2392 -
Rfree-0 -
obs--99.87 %
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)
10.5874-0.68470.34143.204-2.41283.2398-0.06960.13940.15380.0665-0.0042-0.0292-0.08810.20610.07380.0677-0.0633-0.01040.18030.08640.0568-11.5101-23.4996-16.8711
23.9760.88640.51361.5525-0.01882.04180.0446-0.23320.22670.2157-0.08080.0497-0.2118-0.05670.03620.1333-0.02890.06480.01830.01690.0302-15.1204-35.57317.8541
33.43642.1671.96721.69391.51764.6846-0.0489-0.22220.39750.2423-0.00520.3708-0.0523-0.39630.05410.02910.02580.02490.00170.00920.0902-27.4782-13.696-41.7454
42.1044-0.2901-0.14223.5404-0.5092.42850.04210.16620.1657-0.23520.04850.1477-0.0807-0.1193-0.09060.0493-0.0341-0.03340.0262-0.00750.0292-27.5432-17.8957-69.8049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 113
2X-RAY DIFFRACTION2A114 - 299
3X-RAY DIFFRACTION3B15 - 113
4X-RAY DIFFRACTION4B114 - 297

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