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Yorodumi- PDB-1wp5: Crystal structure of the C-terminal domain of DNA topoisomerase IV -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wp5 | ||||||
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Title | Crystal structure of the C-terminal domain of DNA topoisomerase IV | ||||||
Components | topoisomerase IV | ||||||
Keywords | ISOMERASE / broken beta-propeller / hairpin-invaded beta-propeller / six-bladed beta-propeller | ||||||
Function / homology | DNA gyrase/topoisomerase IV, subunit A, C-terminal / 6 Propeller / Neuraminidase / Mainly Beta Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 Å | ||||||
Authors | Hsieh, T.-J. / Farh, L. / Huang, W.M. / Chan, N.-L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis Authors: Hsieh, T.-J. / Farh, L. / Huang, W.M. / Chan, N.-L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wp5.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wp5.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/1wp5 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/1wp5 | 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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-Components
#1: Protein | Mass: 37010.914 Da / Num. of mol.: 1 / Fragment: Topo IV C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: ParC / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: EC: 5.99.1.- |
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#2: 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: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: magnesium acetate, sodium cacodylate, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.95370, 0.97994, 0.97966 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2003 | ||||||||||||
Radiation | Monochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.79→23.3 Å / Num. all: 32512 / Num. obs: 30204 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.096 | ||||||||||||
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 4.2 % / Num. unique all: 1906 / Rsym value: 0.224 / % possible all: 70.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.79→23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.475 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.123 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.942 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.793→1.84 Å / Total num. of bins used: 20 /
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