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- PDB-2x7g: Structure of human serine-arginine-rich protein-specific kinase 2... -

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Basic information

Entry
Database: PDB / ID: 2x7g
TitleStructure of human serine-arginine-rich protein-specific kinase 2 (SRPK2) bound to purvalanol B
ComponentsUNCHARACTERIZED PROTEIN SRPK2
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / MRNA SPLICING / PHOSPHOPROTEIN / MRNA PROCESSING / DIFFERENTIATION / NUCLEOTIDE-BINDING / SPLICEASOME ASSEMBLY / ATP COMPETITIVE INHIBITOR / KINASE / NUCLEUS / ATP-BINDING / SPLICE FACTOR TRAFFICKING
Function / homology
Function and homology information


nuclear speck organization / R-loop processing / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / spliceosomal complex assembly / negative regulation of viral genome replication / positive regulation of viral genome replication / positive regulation of cell cycle / RNA splicing ...nuclear speck organization / R-loop processing / regulation of mRNA processing / regulation of mRNA splicing, via spliceosome / Maturation of nucleoprotein / spliceosomal complex assembly / negative regulation of viral genome replication / positive regulation of viral genome replication / positive regulation of cell cycle / RNA splicing / 14-3-3 protein binding / positive regulation of neuron apoptotic process / angiogenesis / peptidyl-serine phosphorylation / cell differentiation / non-specific serine/threonine protein kinase / intracellular signal transduction / nuclear speck / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / chromatin / positive regulation of gene expression / nucleolus / magnesium ion binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / PURVALANOL B / : / SRSF protein kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPike, A.C.W. / Savitsky, P. / Fedorov, O. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Gileadi, O. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. ...Pike, A.C.W. / Savitsky, P. / Fedorov, O. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Gileadi, O. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Knapp, S.
CitationJournal: To be Published
Title: Structure of Human Serine-Arginine-Rich Protein- Specific Kinase 2 (Srpk2) Bound to Purvalanol B
Authors: Pike, A.C.W. / Savitsky, P. / Fedorov, O. / Krojer, T. / Ugochukwu, E. / von Delft, F. / Gileadi, O. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Knapp, S.
History
DepositionFeb 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNCHARACTERIZED PROTEIN SRPK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,83716
Polymers44,3011
Non-polymers1,53715
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.310, 110.310, 90.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UNCHARACTERIZED PROTEIN SRPK2 / SERINE/THREONINE-PROTEIN KINASE SRPK


Mass: 44300.676 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 62-267,519-699
Source method: isolated from a genetically manipulated source
Details: SYNTHETIC CONSTRUCT ENGINEERED TO REMOVE INTERVENING REGION.
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: C9JQJ0, UniProt: P78362*PLUS, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 126 molecules

#2: Chemical ChemComp-PVB / PURVALANOL B / 2-CHLORO-4-{[2-{[(1R)-1-(HYDROXYMETHYL)-2-METHYLPROPYL]AMINO}-9-(1-METHYLETHYL)-9H-PURIN-6-YL]AMINO}BENZOIC ACID / Cyclin-dependent kinase 2


Mass: 432.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25ClN6O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSYNTHETIC CONSTRUCT WITH 268-518 REMOVED

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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: 3.6 Å3/Da / Density % sol: 65.82 % / Description: NONE
Crystal growpH: 4.75 / Details: 0.5M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH4.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9796
DetectorType: RAYONIX / Detector: CCD / Date: Sep 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→45.21 Å / Num. obs: 22306 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 43.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WBP

1wbp


Resolution: 2.5→45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.893 / SU B: 12.616 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24868 1135 5.1 %RANDOM
Rwork0.18292 ---
obs0.18615 21171 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.352 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 93 111 2969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212919
X-RAY DIFFRACTIONr_bond_other_d0.0010.021981
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9673947
X-RAY DIFFRACTIONr_angle_other_deg0.86534801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7925342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14323.359131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20515488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7421518
X-RAY DIFFRACTIONr_chiral_restr0.0760.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213159
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02602
X-RAY DIFFRACTIONr_nbd_refined0.2140.2548
X-RAY DIFFRACTIONr_nbd_other0.1760.21872
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21373
X-RAY DIFFRACTIONr_nbtor_other0.0850.21439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.45231716
X-RAY DIFFRACTIONr_mcbond_other0.6273695
X-RAY DIFFRACTIONr_mcangle_it4.09152768
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.69281203
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.999121179
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 71 -
Rwork0.281 1541 -
obs--99.26 %
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)
16.9143-1.4692-2.55558.5933.46857.4686-0.24960.93520.1437-0.94610.1099-0.0149-0.40610.10340.13980.3051-0.2373-0.09470.30950.10350.1311-19.325349.5508-12.3388
22.29051.06720.82221.84490.22071.3431-0.16670.35570.0148-0.29630.1874-0.2542-0.05550.3298-0.02070.101-0.04350.00990.1048-0.00720.0741-26.621235.7123-4.2927
31.55710.5526-0.3732.5851.37152.62410.0604-0.158-0.16560.0222-0.0060.11740.1616-0.3168-0.05440.0548-0.0511-0.03630.11120.07080.0586-47.517827.16113.6401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A81 - 131
2X-RAY DIFFRACTION2A132 - 564
3X-RAY DIFFRACTION2A800
4X-RAY DIFFRACTION3A565 - 699

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