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- PDB-1cks: HUMAN CKSHS2 ATOMIC STRUCTURE: A ROLE FOR ITS HEXAMERIC ASSEMBLY ... -

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Basic information

Entry
Database: PDB / ID: 1cks
TitleHUMAN CKSHS2 ATOMIC STRUCTURE: A ROLE FOR ITS HEXAMERIC ASSEMBLY IN CELL CYCLE CONTROL
ComponentsCYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
KeywordsCELL DIVISION
Function / homology
Function and homology information


meiosis I / mitotic cell cycle phase transition / cyclin-dependent protein serine/threonine kinase activator activity / SCF ubiquitin ligase complex / cyclin-dependent protein kinase holoenzyme complex / regulation of mitotic cell cycle / ubiquitin binding / histone binding / fibroblast proliferation / cell division ...meiosis I / mitotic cell cycle phase transition / cyclin-dependent protein serine/threonine kinase activator activity / SCF ubiquitin ligase complex / cyclin-dependent protein kinase holoenzyme complex / regulation of mitotic cell cycle / ubiquitin binding / histone binding / fibroblast proliferation / cell division / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsParge, H.E. / Arvai, A.S. / Tainer, J.A.
CitationJournal: Science / Year: 1993
Title: Human CksHs2 atomic structure: a role for its hexameric assembly in cell cycle control.
Authors: Parge, H.E. / Arvai, A.S. / Murtari, D.J. / Reed, S.I. / Tainer, J.A.
History
DepositionSep 16, 1993Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
B: CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
C: CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9266
Polymers29,6383
Non-polymers2883
Water4,035224
1
A: CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
B: CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
C: CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
hetero molecules

A: CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
B: CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
C: CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,85312
Polymers59,2766
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area23390 Å2
ΔGint-226 kcal/mol
Surface area24520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.100, 57.600, 51.100
Angle α, β, γ (deg.)90.00, 117.40, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.8219, 0.297, 0.4861), (-0.2948, -0.5084, 0.8091), (0.4874, -0.8083, -0.3303)-26.151, 14.739, 70.609
2given(0.835, -0.3081, 0.4559), (0.28, -0.4753, -0.8341), (0.4737, 0.8241, -0.3106)-7.478, 73.046, 23.033
DetailsTHE FOLLOWING TRANSFORMATION WILL GENERATE CHAINS D, E, F FROM CHAINS A, B, C, RESPECTIVELY. CHAINS A, B, C, D, E, AND F FORM A HEXAMER. TRNSF1 3 -1.000000 0.000000 0.000000 53.094002 TRNSF2 3 0.000000 1.000000 0.000000 0.000000 TRNSF3 3 0.000000 0.000000 -1.000000 90.760002

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Components

#1: Protein CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2 /


Mass: 9879.365 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P33552
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
154 %satammonium sulfate1reservoir
250 mMsodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 15146 / % possible obs: 99.9 % / Observed criterion σ(I): 3.2 / Num. measured all: 93995 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→10 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.168 -
obs0.168 13693
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 15 224 2270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.168 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.4

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