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- PDB-3qy2: Crystal structure of the P93A monomer mutant of S. cerevisiae Cks1 -

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Basic information

Entry
Database: PDB / ID: 3qy2
TitleCrystal structure of the P93A monomer mutant of S. cerevisiae Cks1
ComponentsCyclin-dependent kinases regulatory subunit
KeywordsTRANSFERASE REGULATOR / protein kinase activator / ubiquitin binding / transcription / Cdc28 kinase / cell cycle / cyclin-dependent kinase
Function / homology
Function and homology information


regulation of cell cycle G1/S phase transition / cyclin-dependent protein serine/threonine kinase activator activity / SCF ubiquitin ligase complex / protein kinase activator activity / cyclin-dependent protein kinase holoenzyme complex / regulation of mitotic cell cycle / ubiquitin binding / histone binding / cell cycle / cell division ...regulation of cell cycle G1/S phase transition / cyclin-dependent protein serine/threonine kinase activator activity / SCF ubiquitin ligase complex / protein kinase activator activity / cyclin-dependent protein kinase holoenzyme complex / regulation of mitotic cell cycle / ubiquitin binding / histone binding / cell cycle / cell division / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Cyclin-dependent kinases regulatory subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBalog, E.R.M. / Saetern, O.C. / Finch, W. / Hoeft, C.O. / Thai, V. / Harvey, S.L. / Kellogg, D.K. / Rubin, S.M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The structure of a monomeric mutant cks protein reveals multiple functions for a conserved hinge-region proline.
Authors: Balog, E.R. / Saetern, O.C. / Finch, W. / Hoeft, C.O. / Thai, V. / Harvey, S.L. / Kellogg, D.R. / Rubin, S.M.
History
DepositionMar 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Cyclin-dependent kinases regulatory subunit
B: Cyclin-dependent kinases regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8843
Polymers27,6952
Non-polymers1891
Water75742
1
A: Cyclin-dependent kinases regulatory subunit


Theoretical massNumber of molelcules
Total (without water)13,8481
Polymers13,8481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cyclin-dependent kinases regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0372
Polymers13,8481
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Cyclin-dependent kinases regulatory subunit
hetero molecules

B: Cyclin-dependent kinases regulatory subunit
hetero molecules

A: Cyclin-dependent kinases regulatory subunit

A: Cyclin-dependent kinases regulatory subunit


Theoretical massNumber of molelcules
Total (without water)55,7686
Polymers55,3904
Non-polymers3782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
crystal symmetry operation3_554-y+1/2,x+1/2,z-1/41
crystal symmetry operation5_444-x-1/2,y-1/2,-z-1/41
Buried area5620 Å2
ΔGint-16.7 kcal/mol
Surface area22350 Å2
MethodPISA
4
A: Cyclin-dependent kinases regulatory subunit
B: Cyclin-dependent kinases regulatory subunit
hetero molecules

A: Cyclin-dependent kinases regulatory subunit
B: Cyclin-dependent kinases regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7686
Polymers55,3904
Non-polymers3782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4790 Å2
ΔGint-21 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.522, 89.522, 93.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-3585-

FLC

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Components

#1: Protein Cyclin-dependent kinases regulatory subunit / Cell division control protein CKS1


Mass: 13847.542 Da / Num. of mol.: 2 / Fragment: UNP residues 1-117 / Mutation: P93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CKS1, YBR135W, YBR1011 / Production host: Escherichia coli (E. coli) / References: UniProt: P20486
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 0.2 M sodium citrate, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2009
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12295 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 31.167
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.417 / Rsym value: 0.41 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→64.55 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.872 / SU B: 8.687 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27293 1200 9.8 %RANDOM
Rwork0.21148 ---
obs0.21739 11016 99.36 %-
all-12216 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.193 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0 Å2
2---0.3 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.59→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 13 42 1829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211838
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9472488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61722.816103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40715308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4341517
X-RAY DIFFRACTIONr_chiral_restr0.1060.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211435
X-RAY DIFFRACTIONr_mcbond_it0.8651.51050
X-RAY DIFFRACTIONr_mcangle_it1.71321694
X-RAY DIFFRACTIONr_scbond_it2.3183788
X-RAY DIFFRACTIONr_scangle_it3.9244.5794
LS refinement shellResolution: 2.591→2.658 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 101 -
Rwork0.302 710 -
obs--91.23 %

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