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Yorodumi- PDB-1cy8: COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cy8 | ||||||
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Title | COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE AND 3'-THYMIDINE MONOPHOSPHATE | ||||||
Components | DNA TOPOISOMERASE I | ||||||
Keywords | ISOMERASE / DNA TOPOISOMERASE / RELAXING ENZYME | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å | ||||||
Authors | Feinberg, H. / Changela, A. / Mondragon, A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cy8.cif.gz | 130.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cy8.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/1cy8 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/1cy8 | HTTPS FTP |
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-Related structure data
Related structure data | 1cy0C 1cy1C 1cy2C 1cy4C 1cy6C 1cy7C 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: 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.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P06612, DNA topoisomerase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-T3P / |
#4: Chemical | ChemComp-TMP / |
#5: 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: 2.64 Å3/Da / Density % sol: 53.41 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.2M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / pH: 8 / Details: Lima, C.D., (1993) J.Mol.Biol., 232, 1213. | ||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
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: 2.45→30 Å / Num. all: 418613 / Num. obs: 27088 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.255 / % possible all: 98.1 |
Reflection | *PLUS Num. measured all: 418613 |
Reflection shell | *PLUS % possible obs: 98.1 % |
-Processing
Software |
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Refinement | Resolution: 2.45→19.82 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1578413.46 / 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: 25.79 Å2 / ksol: 0.306 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.025 / 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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