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Yorodumi- PDB-2b9s: Crystal Structure of heterodimeric L. donovani topoisomerase I-va... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b9s | ||||||
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Title | Crystal Structure of heterodimeric L. donovani topoisomerase I-vanadate-DNA complex | ||||||
Components |
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Keywords | ISOMERASE/DNA / topoisomerase I / vanadate complex / ISOMERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Davies, D.R. / Hol, W.G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: The Structure of the Transition State of the Heterodimeric Topoisomerase I of Leishmania donovani as a Vanadate Complex with Nicked DNA. Authors: Davies, D.R. / Mushtaq, A. / Interthal, H. / Champoux, J.J. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b9s.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b9s.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/2b9s ftp://data.pdbj.org/pub/pdb/validation_reports/b9/2b9s | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a heterodimer consisting of one copy each of the large and small subunits and a DNA duplex. |
-Components
-DNA chain , 3 types, 3 molecules CDE
#1: DNA chain | Mass: 3061.057 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3684.453 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 6705.373 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 2 types, 2 molecules AB
#4: Protein | Mass: 50903.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: topoisomerase I, large subunit (LdTOP1L) / Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: GenBank: 5305782, UniProt: Q9GPZ9*PLUS, DNA topoisomerase |
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#5: Protein | Mass: 7138.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: topoisomerase I, small subunit (LdTOP1S) / Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: GenBank: 17528932, UniProt: Q8WQM6*PLUS, DNA topoisomerase |
-Non-polymers , 2 types, 131 molecules
#6: Chemical | ChemComp-VO4 / |
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#7: 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: 3.38 Å3/Da / Density % sol: 63.66 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.1 Details: 18% PEG 3350, 0.2 M Na2HPO4, 0.1 M LiCl, pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. all: 43803 / Num. obs: 43803 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Χ2: 0.953 |
Reflection shell | Resolution: 2.27→2.35 Å / % possible obs: 71.6 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.408 / Num. measured obs: 3207 / Χ2: 0.812 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→43.48 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.412 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.498 Å2
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Refinement step | Cycle: LAST / Resolution: 2.27→43.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.273→2.332 Å / Total num. of bins used: 20
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