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Open data
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Basic information
Entry | Database: PDB / ID: 1cy4 | ||||||
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Title | COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpTp3' | ||||||
![]() | DNA TOPOISOMERASE I | ||||||
![]() | ISOMERASE / DNA TOPOISOMERASE / RELAXING ENZYME | ||||||
Function / homology | ![]() DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Feinberg, H. / Changela, A. / Mondragon, A. | ||||||
![]() | ![]() Title: Protein-nucleotide interactions in E. coli DNA topoisomerase I. Authors: Feinberg, H. / Changela, A. / Mondragon, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.3 KB | Display | ![]() |
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PDB format | ![]() | 99.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.4 KB | Display | ![]() |
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Full document | ![]() | 464.9 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cy0C ![]() 1cy1C ![]() 1cy2C ![]() 1cy6C ![]() 1cy7C ![]() 1cy8C C: citing same article ( |
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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: Protein | Mass: 67542.500 Da / Num. of mol.: 1 Fragment: 67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-TMP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.42 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.2M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Details: and 14 degrees centigrade | ||||||||||||||||||||
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: IMAGE PLATE / Date: May 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. all: 335586 / Num. obs: 24076 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.077 |
Reflection shell | Resolution: 2.55→2.64 Å / Rmerge(I) obs: 0.284 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 335586 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Resolution: 2.55→19.76 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1421041.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Stereochemistry target values: R. A. ENGH AND R. HUBER, ACTA CRYST. SECT. A., 1991 Details: REFINEMENT DONE WITH REFMAC. THE SOLVENT CORRECTION WAS CALCULATED WITH XPLOR AND APPLIED IN REFMAC. FINAL PARAMETERS OBTAINED WITH CNS 0.9
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.96 Å2 / ksol: 0.308 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: 'X-PLOR,REFMAC,CNS 0.9' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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