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- PDB-1dkt: CKSHS1: HUMAN CYCLIN DEPENDENT KINASE SUBUNIT, TYPE 1 COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 1dkt
TitleCKSHS1: HUMAN CYCLIN DEPENDENT KINASE SUBUNIT, TYPE 1 COMPLEX WITH METAVANADATE
ComponentsCYCLIN DEPENDENT KINASE SUBUNIT, TYPE 1Cyclin-dependent kinase
KeywordsCELL DIVISION
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
META VANADATE / Cyclin-dependent kinases regulatory subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsBourne, Y. / Arvai, A.S. / Tainer, J.A.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of the human cell cycle protein CksHs1: single domain fold with similarity to kinase N-lobe domain.
Authors: Arvai, A.S. / Bourne, Y. / Hickey, M.J. / Tainer, J.A.
#1: Journal: Proteins / Year: 1995
Title: Crystallization and Preliminary Crystallographic Study of Human Ckshs1: A Cell Cycle Regulatory Protein
Authors: Arvai, A.S. / Bourne, Y. / Williams, D. / Reed, S.I. / Tainer, J.A.
History
DepositionNov 22, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _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 1
B: CYCLIN DEPENDENT KINASE SUBUNIT, TYPE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0193
Polymers19,3582
Non-polymers6611
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-10 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.000, 94.000, 131.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.18391, -0.95094, -0.248777), (-0.950274, -0.236717, 0.202346), (-0.251309, 0.199193, -0.947189)
Vector: 47.5093, 54.274, 19.3576)
DetailsTHE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 5 .. B 75 A 5 .. A 75 0.905

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Components

#1: Protein CYCLIN DEPENDENT KINASE SUBUNIT, TYPE 1 / Cyclin-dependent kinase / CKSHS1


Mass: 9679.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-ZI / References: UniProt: P61024
#2: Chemical ChemComp-V7O / META VANADATE


Mass: 660.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O19V7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.33 Å3/Da / Density % sol: 71.61 %
Crystal
*PLUS
Density % sol: 72 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %(w/v)PEG40001reservoir
215-30 mg/mlprotein1drop
3sodium metavanadate1drop0.0012ml
4reservoir solution1drop0.008ml

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 7655 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 25
Reflection shellResolution: 2.9→3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5 / % possible all: 80
Reflection
*PLUS
Redundancy: 3 % / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 80 % / Redundancy: 2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.9→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.258 -5 %
Rwork0.195 --
obs0.195 6943 94 %
Refinement stepCycle: LAST / Resolution: 2.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 26 62 1325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.9
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
Solvent computation
*PLUS
Displacement parameters
*PLUS

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