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- PDB-1buh: CRYSTAL STRUCTURE OF THE HUMAN CDK2 KINASE COMPLEX WITH CELL CYCL... -

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Basic information

Entry
Database: PDB / ID: 1buh
TitleCRYSTAL STRUCTURE OF THE HUMAN CDK2 KINASE COMPLEX WITH CELL CYCLE-REGULATORY PROTEIN CKSHS1
Components
  • PROTEIN (CDK2 HUMAN)
  • PROTEIN (CKSHS1 HUMAN)
KeywordsTRANSFERASE
Function / homology
Function and homology information


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 / SCF(Skp2)-mediated degradation of p27/p21 / Cyclin D associated events in G1 / histone binding / fibroblast proliferation ...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 / SCF(Skp2)-mediated degradation of p27/p21 / Cyclin D associated events in G1 / histone binding / fibroblast proliferation / cell division / regulation of DNA-templated transcription / protein kinase binding / nucleoplasm
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 / Replication initiator protein RctB, central region / RctB, helix turn helix domain ...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 / Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Cyclin-dependent kinases regulatory subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBourne, Y. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure and mutational analysis of the human CDK2 kinase complex with cell cycle-regulatory protein CksHs1.
Authors: Bourne, Y. / Watson, M.H. / Hickey, M.J. / Holmes, W. / Rocque, W. / Reed, S.I. / Tainer, J.A.
History
DepositionSep 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 9, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CDK2 HUMAN)
B: PROTEIN (CKSHS1 HUMAN)


Theoretical massNumber of molelcules
Total (without water)43,6562
Polymers43,6562
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-7 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.800, 69.950, 60.530
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (CDK2 HUMAN)


Mass: 33976.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P24941
#2: Protein PROTEIN (CKSHS1 HUMAN)


Mass: 9679.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRK171 / Production host: Escherichia coli (E. coli) / References: UniProt: P61024
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growpH: 7.5
Details: 17-19% MEPEG 5K, 100 MM TRIS-HCL PH 7.5, 100 MM KCL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
217-19 %MEPEG50001reservoir
3100 mMTris1reservoir
4100 mM1reservoirKCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1995
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 84909 / % possible obs: 97 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1
Reflection
*PLUS
Num. obs: 13023 / Num. measured all: 84909 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PERSONAL COMMUNICATION

Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 612 5 %RANDOM
Rwork0.19 ---
obs0.19 13011 97 %-
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 0 127 3043
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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
LS refinement shellResolution: 2.6→2.7 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.31 64 5 %
Rwork0.28 1478 -
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / Rfactor Rfree: 0.31 / % reflection Rfree: 5 % / Rfactor Rwork: 0.28

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