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- PDB-1qb3: CRYSTAL STRUCTURE OF THE CELL CYCLE REGULATORY PROTEIN CKS1 -

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Basic information

Entry
Database: PDB / ID: 1qb3
TitleCRYSTAL STRUCTURE OF THE CELL CYCLE REGULATORY PROTEIN CKS1
ComponentsCYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT
KeywordsCELL CYCLE / CELL CYCLE MUTAGENESIS DOMAIN SWAPPING / 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 division / regulation of transcription by RNA polymerase II ...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 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
Cyclin-dependent kinases regulatory subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsBourne, Y. / Watson, M.H. / Arvai, A.S. / Bernstein, S.L. / Reed, S.I. / Tainer, J.A.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure and mutational analysis of the Saccharomyces cerevisiae cell cycle regulatory protein Cks1: implications for domain swapping, anion binding and protein interactions.
Authors: Bourne, Y. / Watson, M.H. / Arvai, A.S. / Bernstein, S.L. / Reed, S.I. / Tainer, J.A.
History
DepositionApr 30, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Aug 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT
B: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT
C: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT


Theoretical massNumber of molelcules
Total (without water)53,4503
Polymers53,4503
Non-polymers00
Water43224
1
A: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT
B: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT


Theoretical massNumber of molelcules
Total (without water)35,6332
Polymers35,6332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT

C: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT


Theoretical massNumber of molelcules
Total (without water)35,6332
Polymers35,6332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_556-y,-x,-z+5/31
3
B: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT

B: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT

B: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT

B: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT


Theoretical massNumber of molelcules
Total (without water)71,2674
Polymers71,2674
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation9_556-x,-x+y,-z+4/31
crystal symmetry operation12_556x,x-y,-z+4/31
Buried area10650 Å2
ΔGint-85 kcal/mol
Surface area28800 Å2
MethodPISA
4
A: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT
C: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT


Theoretical massNumber of molelcules
Total (without water)35,6332
Polymers35,6332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
B: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT

B: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT


Theoretical massNumber of molelcules
Total (without water)35,6332
Polymers35,6332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.810, 105.810, 165.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT


Mass: 17816.715 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P20486
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 4K, 5% NASCN AND 0.1 M IMIDAZOLE/MALATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
220 %PEG40001drop
35 %sat1dropNaSCN
40.1 Mimidazole/malate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→12 Å / Num. all: 10366 / Num. obs: 10218 / % possible obs: 91 % / Observed criterion σ(F): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.405 / % possible all: 93.7
Reflection
*PLUS
Num. obs: 10366 / Num. measured all: 243609

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementResolution: 3→12 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.291 539 -
Rwork0.216 --
obs-10218 89.9 %
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 0 24 2829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.9
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg24.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.216 / Num. reflection obs: 10366
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.9

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