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- PDB-6u69: Crystal structure of Yck2 from Candida albicans, apoenzyme -

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Basic information

Entry
Database: PDB / ID: 6u69
TitleCrystal structure of Yck2 from Candida albicans, apoenzyme
ComponentsSerine/threonine protein kinase
KeywordsTRANSFERASE / casein kinase 1 / Yck2 / kinase / structural genomics / center for structural genomics of infectious diseases / niaid / national institute of allergy and infectious diseases / CSGID
Function / homology
Function and homology information


regulation of single-species biofilm formation / regulation of cell wall organization or biogenesis / hyphal growth / regulation of filamentous growth / biological process involved in interaction with host / endocytosis / extracellular vesicle / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / signal transduction ...regulation of single-species biofilm formation / regulation of cell wall organization or biogenesis / hyphal growth / regulation of filamentous growth / biological process involved in interaction with host / endocytosis / extracellular vesicle / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane
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 ...: / 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
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / 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: Cell Chem Biol / Year: 2020
Title: Overcoming Fungal Echinocandin Resistance through Inhibition of the Non-essential Stress Kinase Yck2.
Authors: Caplan, T. / Lorente-Macias, A. / Stogios, P.J. / Evdokimova, E. / Hyde, S. / Wellington, M.A. / Liston, S. / Iyer, K.R. / Puumala, E. / Shekhar-Guturja, T. / Robbins, N. / Savchenko, A. / ...Authors: Caplan, T. / Lorente-Macias, A. / Stogios, P.J. / Evdokimova, E. / Hyde, S. / Wellington, M.A. / Liston, S. / Iyer, K.R. / Puumala, E. / Shekhar-Guturja, T. / Robbins, N. / Savchenko, A. / Krysan, D.J. / Whitesell, L. / Zuercher, W.J. / Cowen, L.E.
History
DepositionAug 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 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: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6214
Polymers35,3971
Non-polymers2243
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.771, 91.771, 119.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Serine/threonine protein kinase


Mass: 35397.254 Da / Num. of mol.: 1
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: YCK2, orf19.7001, CAALFM_C305650WA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: A0A1D8PKB4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8, 25 mM magnesium chloride, 22% (w/v) PEG3350
PH range: 8

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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: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.61→30 Å / Num. obs: 11498 / % possible obs: 100 % / Redundancy: 5.8 % / Biso Wilson estimate: 49.1 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.031 / Net I/σ(I): 20.58
Reflection shellResolution: 2.61→2.65 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 584 / CC1/2: 0.97 / Rpim(I) all: 0.241 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X18

5x18


Resolution: 2.61→29.14 Å / SU ML: 0.3037 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 28.394
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 579 5.06 %RANDOM
Rwork0.1907 ---
obs0.1935 11449 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.82 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 12 113 2594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392537
X-RAY DIFFRACTIONf_angle_d0.59913426
X-RAY DIFFRACTIONf_chiral_restr0.0414358
X-RAY DIFFRACTIONf_plane_restr0.0036448
X-RAY DIFFRACTIONf_dihedral_angle_d22.5891956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.870.28851380.2382735X-RAY DIFFRACTION100
2.87-3.290.27821510.232712X-RAY DIFFRACTION99.97
3.29-4.140.25091480.18962719X-RAY DIFFRACTION100
4.14-29.140.22181420.16522704X-RAY DIFFRACTION99.93
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)
11.772866386112.92746701836-0.1725116374485.51786292185-0.2232765747730.867091921468-0.1097329617610.02268433888780.5644265612-0.4756324958060.07906409759390.340210470574-0.129045912186-0.2442146207530.002496989290650.3068289719380.0724427403991-0.02801946577690.375289142951-0.001107531460250.60140397633222.5619890657-17.5245489281-10.0479028316
24.59290005477-1.024499502540.2115790165462.889776164120.240835772842.127240283770.1603594054280.136381192840.0210198584445-0.137350597083-0.03412946151590.09967317659970.126691026672-0.281009081684-0.1343101175360.273723004975-0.08657774219710.01971762340350.3485699640930.03644219603780.33755255032612.9182580676-34.7601064574-9.16807854593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 193 )
2X-RAY DIFFRACTION2chain 'A' and (resid 194 through 342 )

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