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- PDB-6o6q: Crystal structure of Cka1p, a casein kinase 2 alpha ortholog from... -

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Basic information

Entry
Database: PDB / ID: 6o6q
TitleCrystal structure of Cka1p, a casein kinase 2 alpha ortholog from Candida albicans
ComponentsCasein kinase 2 catalytic subunit
KeywordsTRANSFERASE / kinase / alpha/beta fold / fungus / pathogenesis / National Institute of Allergy and Infectious Diseases / NIAID / National Institutes of Health / NIH / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / protein kinase CK2 complex / peptidyl-threonine phosphorylation / peptidyl-serine phosphorylation / regulation of cell cycle / protein serine/threonine kinase activity / DNA damage response / ATP binding / nucleus / cytosol
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
ADENOSINE MONOPHOSPHATE / Casein kinase 2 catalytic subunit
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of Cka1p, a casein kinase 2 alpha ortholog from Candida albicans
Authors: Stogios, P.J.
History
DepositionMar 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Casein kinase 2 catalytic subunit
B: Casein kinase 2 catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,49317
Polymers80,0462
Non-polymers1,44615
Water3,153175
1
A: Casein kinase 2 catalytic subunit
B: Casein kinase 2 catalytic subunit
hetero molecules

A: Casein kinase 2 catalytic subunit
B: Casein kinase 2 catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,98534
Polymers160,0924
Non-polymers2,89330
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area12520 Å2
ΔGint-209 kcal/mol
Surface area58710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.690, 125.690, 229.719
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Casein kinase 2 catalytic subunit


Mass: 40023.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: CKA1, CAALFM_CR10660WA, orf19.7652 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Gold / References: UniProt: A0A1D8PUA2

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Non-polymers , 5 types, 190 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2 M ammonium sulfate, 0.1 M sodium citrate pH 6.1, 1 mM AMP-PNP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.66→35 Å / Num. obs: 31301 / % possible obs: 98.9 % / Redundancy: 18.3 % / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.043 / Net I/σ(I): 18.57
Reflection shellResolution: 2.66→2.71 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.004 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 1254 / CC1/2: 0.787 / Rpim(I) all: 0.305 / % possible all: 82.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bqc

3bqc


Resolution: 2.7→34.598 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2873 2360 5.02 %RANDOM
Rwork0.2335 ---
obs0.2361 47037 84.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→34.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 82 175 5755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045706
X-RAY DIFFRACTIONf_angle_d0.6477696
X-RAY DIFFRACTIONf_dihedral_angle_d21.3252169
X-RAY DIFFRACTIONf_chiral_restr0.054805
X-RAY DIFFRACTIONf_plane_restr0.003962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.75520.4108640.28321076X-RAY DIFFRACTION35
2.7552-2.81510.3123680.30471341X-RAY DIFFRACTION43
2.8151-2.88050.3188960.30981838X-RAY DIFFRACTION59
2.8805-2.95250.34221150.3152185X-RAY DIFFRACTION70
2.9525-3.03230.40131230.32952348X-RAY DIFFRACTION76
3.0323-3.12150.33811350.29552515X-RAY DIFFRACTION81
3.1215-3.22210.32291450.29852709X-RAY DIFFRACTION87
3.2221-3.33720.35691590.27172985X-RAY DIFFRACTION96
3.3372-3.47070.31791650.25333081X-RAY DIFFRACTION99
3.4707-3.62850.29591620.23183112X-RAY DIFFRACTION99
3.6285-3.81960.28031570.21743107X-RAY DIFFRACTION99
3.8196-4.05860.2811610.2043045X-RAY DIFFRACTION98
4.0586-4.37140.23571550.18063061X-RAY DIFFRACTION98
4.3714-4.81020.2241610.17883060X-RAY DIFFRACTION98
4.8102-5.50390.24811620.20183069X-RAY DIFFRACTION99
5.5039-6.92520.32021660.25323078X-RAY DIFFRACTION99
6.9252-34.60120.25251660.23253067X-RAY DIFFRACTION98
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)
11.82230.18190.95661.67810.25893.7075-0.0739-0.10710.1079-0.06180.07380.1489-0.0138-0.335-0.00690.2091-0.0103-0.00080.18460.0460.25942.607629.5052-6.9179
20.55740.1333-0.12890.9896-0.04781.3591-0.0649-0.0226-0.29920.46610.3324-0.16080.93061.09410.01130.90510.2598-0.10690.512-0.15370.588175.2078-4.449423.1793
31.94860.06740.69432.26530.1233.8914-0.00150.33960.06770.14540.1264-0.1980.14440.880.02590.24810.0635-0.03590.3267-0.07920.263574.053616.946521.311
40.49460.1880.11042.1042-0.83151.64080.09010.0629-0.0542-0.64690.11270.44120.5878-0.40480.00060.7655-0.0191-0.05090.39210.04150.464542.40789.9343-17.7681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 134 through 333 )
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 91 )
3X-RAY DIFFRACTION3chain 'B' and (resid 92 through 333 )
4X-RAY DIFFRACTION4chain 'A' and (resid 4 through 133 )

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