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- PDB-2nov: Breakage-reunion domain of S.pneumoniae topo IV: crystal structur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nov | ||||||
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Title | Breakage-reunion domain of S.pneumoniae topo IV: crystal structure of a gram-positive quinolone target | ||||||
![]() | DNA topoisomerase 4 subunit A | ||||||
![]() | ISOMERASE / protein / ParC / topo IV / gram-positive bacteria / quinolone target / DNA binding / DNA cleavage | ||||||
Function / homology | ![]() DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Laponogov, I. / Veselkov, D.A. / Sohi, M.K. / Pan, X.S. / Achari, A. / Yang, C. / Ferrara, J.D. / Fisher, L.M. / Sanderson, M.R. | ||||||
![]() | ![]() Title: Breakage-Reunion Domain of Streptococcus pneumoniae Topoisomerase IV: Crystal Structure of a Gram-Positive Quinolone Target. Authors: Laponogov, I. / Veselkov, D.A. / Sohi, M.K. / Pan, X.S. / Achari, A. / Yang, C. / Ferrara, J.D. / Fisher, L.M. / Sanderson, M.R. #1: ![]() Title: The Structure of the ParC Subunit of Topoisomerase IV from Streptococcus pneumoniae Authors: Laponogov, I. / Veselkov, D.A. / Sohi, M.K. / Pan, X.S. / Fisher, L.M. / Sanderson, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 341.6 KB | Display | ![]() |
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PDB format | ![]() | 277.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460 KB | Display | ![]() |
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Full document | ![]() | 481.7 KB | Display | |
Data in XML | ![]() | 57.5 KB | Display | |
Data in CIF | ![]() | 79.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ab4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a dimer generated by a) A and B chains b) C and D chains (two biological dimers in the asymmetric unit) |
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Components
#1: Protein | Mass: 56455.434 Da / Num. of mol.: 4 / Fragment: 55-kDa N-terminal fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P72525, UniProt: Q3HYJ3*PLUS, EC: 5.99.1.- #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: The purified ParC55 protein was dialyzed against 20 mM Tris-HCl, pH 7.0, 200 mM NaCl, 10% glycerol, 1 mM beta-mercaptoethanol, 0.05% NaN3 then concentrated to 3-4 mg/ml. Hanging drops were ...Details: The purified ParC55 protein was dialyzed against 20 mM Tris-HCl, pH 7.0, 200 mM NaCl, 10% glycerol, 1 mM beta-mercaptoethanol, 0.05% NaN3 then concentrated to 3-4 mg/ml. Hanging drops were formed by mixing equal volumes of protein and crystallization solutions (100 mM Tris-HCl, pH 5.5, 200 mM NaCl, 1 mM beta-mercaptoethanol, 0.05% NaN3 and 10% of 1:1 ethanol-isopropanol as precipitant). , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: two cylindrical parabolic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91694 Å / Relative weight: 1 |
Reflection twin | Type: hemihedral / Operator: k,-h,l / Fraction: 0.323 |
Reflection | Highest resolution: 2.67 Å / Num. obs: 85197 / Redundancy: 5.4 % / Rsym value: 0.093 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AB4 Resolution: 2.67→500 Å Details: Refinement was performed using twinning operator (k,-h,l) and twinning fraction of 0.323
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Solvent computation | Bsol: 13.223 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.915 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.67→500 Å
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Refine LS restraints |
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Xplor file |
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