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Yorodumi- PDB-1buh: CRYSTAL STRUCTURE OF THE HUMAN CDK2 KINASE COMPLEX WITH CELL CYCL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1buh | ||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN CDK2 KINASE COMPLEX WITH CELL CYCLE-REGULATORY PROTEIN CKSHS1 | ||||||
Components |
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Keywords | TRANSFERASE | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Bourne, Y. / Tainer, J.A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1buh.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1buh.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 1buh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1buh_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 1buh_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 1buh_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1buh_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/1buh ftp://data.pdbj.org/pub/pdb/validation_reports/bu/1buh | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1995 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PERSONAL COMMUNICATION Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.7 Å / Total num. of bins used: 8
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Xplor file | Serial 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
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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 |