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Yorodumi- PDB-1k4s: HUMAN DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k4s | ||||||
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Title | HUMAN DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | ||||||
Components |
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Keywords | ISOMERASE/DNA / Complex (ISOMERASE-DNA) / DNA / Topoisomerase I / ISOMERASE-DNA complex | ||||||
Function / homology | Function and homology information 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 / male germ cell nucleus / chromosome segregation ...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 / male germ cell nucleus / chromosome segregation / protein-DNA complex / circadian regulation of gene expression / P-body / fibrillar center / circadian rhythm / chromosome / single-stranded DNA binding / double-stranded DNA binding / peptidyl-serine phosphorylation / perikaryon / DNA replication / chromatin remodeling / response to xenobiotic stimulus / phosphorylation / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Staker, B.L. / Hjerrild, K. / Feese, M.D. / Behnke, C.A. / Burgin Jr., A.B. / Stewart, L.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: The mechanism of topoisomerase I poisoning by a camptothecin analog Authors: Staker, B.L. / Hjerrild, K. / Feese, M.D. / Behnke, C.A. / Burgin Jr., A.B. / Stewart, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k4s.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k4s.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 1k4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k4s_validation.pdf.gz | 400 KB | Display | wwPDB validaton report |
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Full document | 1k4s_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 1k4s_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 1k4s_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/1k4s ftp://data.pdbj.org/pub/pdb/validation_reports/k4/1k4s | HTTPS FTP |
-Related structure data
Related structure data | 1k4tC 1a36S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3284.796 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4138.985 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 7721.218 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Protein | Mass: 70248.023 Da / Num. of mol.: 1 Fragment: Core Domain and C-Terminal Domain, Residues 174-765 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, DNA topoisomerase |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 8000, Tris-HCl, Na/K Phosphate, KCl, DTT, VAPOR DIFFUSION, SITTING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 16 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 18471 / Num. obs: 18471 / % possible obs: 85.9 % / Rsym value: 0.13 |
Reflection shell | Resolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2.95 / Rsym value: 0.13 / % possible all: 69.5 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 17874 / Rmerge(I) obs: 0.13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A36 Resolution: 3.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 41.78 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.217 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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