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Yorodumi- PDB-1t4w: Structural Differences in the DNA Binding Domains of Human p53 an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t4w | ||||||
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Title | Structural Differences in the DNA Binding Domains of Human p53 and its C. elegans Ortholog Cep-1: Structure of C. elegans Cep-1 | ||||||
Components | C.Elegans p53 tumor suppressor-like transcription factor | ||||||
Keywords | TRANSCRIPTION / DNA-Binding Domain | ||||||
Function / homology | Function and homology information meiotic chromosome segregation / response to starvation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / transcription repressor complex / determination of adult lifespan / intrinsic apoptotic signaling pathway in response to DNA damage / response to oxidative stress / sequence-specific DNA binding / response to hypoxia ...meiotic chromosome segregation / response to starvation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / transcription repressor complex / determination of adult lifespan / intrinsic apoptotic signaling pathway in response to DNA damage / response to oxidative stress / sequence-specific DNA binding / response to hypoxia / DNA-binding transcription factor activity / nucleolus / regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.1 Å | ||||||
Authors | Huyen, Y. / Jeffrey, P.D. / Derry, W.B. / Rothman, J.H. / Pavletich, N.P. / Stavridi, E.S. / Halazonetis, T.D. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Structural Differences in the DNA Binding Domains of Human p53 and Its C. elegans Ortholog Cep-1. Authors: Huyen, Y. / Jeffrey, P.D. / Derry, W.B. / Rothman, J.H. / Pavletich, N.P. / Stavridi, E.S. / Halazonetis, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t4w.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t4w.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 1t4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/1t4w ftp://data.pdbj.org/pub/pdb/validation_reports/t4/1t4w | HTTPS FTP |
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-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: 23543.039 Da / Num. of mol.: 1 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q20646 |
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#2: Chemical | ChemComp-ZN / |
#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: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.2 Details: Sodium Citrate, isopropyl alcohol, DTT, BTP, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 23, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 16384 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1522442.61 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.3891 Å2 / ksol: 0.396942 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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