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Yorodumi- PDB-1cy9: CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cy9 | ||||||
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Title | CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM | ||||||
Components | DNA TOPOISOMERASE ITopoisomerase | ||||||
Keywords | ISOMERASE / DNA TOPOISOMERASE / DECATENATING 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: 1.8 Å | ||||||
Authors | Feinberg, H. / Lima, C. / Mondragon, A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Conformational changes in E. coli DNA topoisomerase I. Authors: Feinberg, H. / Lima, C.D. / Mondragon, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cy9.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cy9.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/1cy9 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/1cy9 | HTTPS FTP |
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-Related 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: 29659.596 Da / Num. of mol.: 2 / Fragment: 30 KDA FRAGMENT COMPRISING DOMAINS II AND III 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 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 11-13%(W/V) PEG 3500, 20MM MES PH 6.0, 50MM KCL, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||
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: APS / Beamline: 5ID-B / Wavelength: 1.0038 |
Detector | Detector: CCD / Date: Nov 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0038 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 237667 / Num. obs: 54367 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.255 / % possible all: 76.5 |
Reflection | *PLUS Num. measured all: 237667 |
Reflection shell | *PLUS % possible obs: 76.5 % |
-Processing
Software |
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Refinement | Resolution: 1.8→27.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 12805834.68 / 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: MOST OF THE REFINEMENT DONE WITH REFMAC. SOLVENT CORRECTION WITH XPLOR. FINAL REFINEMENT WITH CNS 0.9
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Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→27.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: 'REFMAC, XPLOR AND CNS 0.9' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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