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- PDB-6k3l: Crystal structure of CX-4945 bound Cka1 from C. neoformans -

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Basic information

Entry
Database: PDB / ID: 6k3l
TitleCrystal structure of CX-4945 bound Cka1 from C. neoformans
ComponentsCMGC/CK2 protein kinase
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


regulation of transcription by RNA polymerase III / regulation of transcription by RNA polymerase I / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / metal ion binding ...regulation of transcription by RNA polymerase III / regulation of transcription by RNA polymerase I / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / 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 ...Casein Kinase 2, subunit alpha / 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
Chem-3NG / Casein kinase II subunit alpha / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsCho, H.S. / Yoo, Y.
CitationJournal: Sci Rep / Year: 2019
Title: Structural analysis of fungal pathogenicity-related casein kinase alpha subunit, Cka1, in the human fungal pathogen Cryptococcus neoformans.
Authors: Ong, B.X. / Yoo, Y. / Han, M.G. / Park, J.B. / Choi, M.K. / Choi, Y. / Shin, J.S. / Bahn, Y.S. / Cho, H.S.
History
DepositionMay 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / entity ...audit_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CMGC/CK2 protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0273
Polymers39,5811
Non-polymers4462
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.762, 95.395, 94.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CMGC/CK2 protein kinase / Casein kinase II subunit alpha


Mass: 39580.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05694
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: J9VNH4, UniProt: A0A226BA59*PLUS
#2: Chemical ChemComp-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 349.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 30 %(w/v) PEG 4000, 30%(w/v) dextran sulfate sodium salt, 5mM CX-4945

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.09→65.79 Å / Num. obs: 23770 / % possible obs: 97 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02506 / Net I/σ(I): 15.7
Reflection shellResolution: 2.094→2.169 Å / Rmerge(I) obs: 0.2672 / Num. unique obs: 1908 / CC1/2: 0.884

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LP4

1lp4


Resolution: 2.09→47.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.085 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 1995 8.4 %RANDOM
Rwork0.18673 ---
obs0.18936 21739 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.927 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.09→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 30 99 2868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132842
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172598
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.6583845
X-RAY DIFFRACTIONr_angle_other_deg1.4951.5896011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9055328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55321.657169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98815496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3581522
X-RAY DIFFRACTIONr_chiral_restr0.0880.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02656
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7633.6281316
X-RAY DIFFRACTIONr_mcbond_other2.7633.6251314
X-RAY DIFFRACTIONr_mcangle_it3.8715.4271642
X-RAY DIFFRACTIONr_mcangle_other3.875.4311643
X-RAY DIFFRACTIONr_scbond_it4.0014.1071526
X-RAY DIFFRACTIONr_scbond_other4.0014.1021523
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0975.9632198
X-RAY DIFFRACTIONr_long_range_B_refined8.17268.26511814
X-RAY DIFFRACTIONr_long_range_B_other8.17168.26711778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.094→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 108 -
Rwork0.289 1241 -
obs--76.13 %

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