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Open data
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Basic information
Entry | Database: PDB / ID: 1nh3 | ||||||
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Title | Human Topoisomerase I Ara-C Complex | ||||||
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![]() | ISOMERASE/DNA / Ara-C / protein-DNA complex / DNA damage / isomerase / ISOMERASE-DNA COMPLEX | ||||||
Function / homology | ![]() DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / phosphorylation / male germ cell nucleus ...DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / phosphorylation / male germ cell nucleus / chromosome segregation / protein-DNA complex / P-body / circadian regulation of gene expression / fibrillar center / circadian rhythm / chromosome / single-stranded DNA binding / double-stranded DNA binding / peptidyl-serine phosphorylation / perikaryon / DNA replication / response to xenobiotic stimulus / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / protein serine/threonine kinase activity / chromatin binding / nucleolus / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chrencik, J.E. / Burgin, A.B. / Pommier, Y. / Stewart, L. / Redinbo, M.R. | ||||||
![]() | ![]() Title: Structural Impact of the Leukemia Drug 1-beta-D-Arabinofuranosylcytosine (Ara-C) on the Covalent Human Topoisomerase I-DNA Complex Authors: Chrencik, J.E. / Burgin, A.B. / Pommier, Y. / Stewart, L. / Redinbo, M.R. | ||||||
History |
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Remark 999 | SEQUENCE The DNA (duplex oligo) was added to the protein during crystallization. At this time, the ...SEQUENCE The DNA (duplex oligo) was added to the protein during crystallization. At this time, the protein initiates a transesterification reaction in which one strand of DNA is broken into chains B and C, and the protein chain A is covalently linked to the DNA through residue 723. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.9 KB | Display | ![]() |
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PDB format | ![]() | 97.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1a31S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3017.004 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3564.368 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA/RNA hybrid | Mass: 6580.128 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Protein | Mass: 66733.867 Da / Num. of mol.: 1 / Fragment: Core Subdomain, C-Terminal Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.41 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 276 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: Tris, Magnesium Chloride, PEG 400, DTT, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 276K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Details: Redinbo, M.R., (1998) Science, 279, 1504. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 18, 2001 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 13878 / Num. obs: 13878 / % possible obs: 69.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.1→3.21 Å / % possible all: 54.7 |
Reflection | *PLUS Lowest resolution: 100 Å / Redundancy: 12.2 % / Num. measured all: 169504 / Rmerge(I) obs: 0.135 |
Reflection shell | *PLUS Lowest resolution: 3.2 Å / % possible obs: 54.7 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1A31 Resolution: 3.1→44.29 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.48 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.71 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→44.29 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 100 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.309 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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