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Yorodumi- PDB-2inr: Crystal structure of a 59 kDa fragment of topoisomerase IV subuni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2inr | ||||||
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Title | Crystal structure of a 59 kDa fragment of topoisomerase IV subunit A (GrlA) from Staphylococcus aureus | ||||||
Components | DNA topoisomerase 4 subunit ATopoisomerase | ||||||
Keywords | ISOMERASE / topoisomerase II fold | ||||||
Function / homology | Function and homology information 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 Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Carr, S.B. | ||||||
Citation | Journal: To be Published Title: Crystal structure of a 59 kDa fragment of topoisomerase IV subunit A (GrlA) from Staphylococcus aureus Authors: Carr, S.B. / Makris, G. / Thomas, C.D. / Phillips, S.E.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2inr.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2inr.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 2inr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/2inr ftp://data.pdbj.org/pub/pdb/validation_reports/in/2inr | HTTPS FTP |
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-Related structure data
Related structure data | 1ab4S S: Starting model for refinement |
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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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Details | GrlA is dimeric, 1 monomer per asymmetric unit second monomer is generated by two-fold axis x -y z |
-Components
#1: Protein | Mass: 58648.875 Da / Num. of mol.: 1 / Fragment: 59 kDa fragment of GrlA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: RN4220 / Gene: parC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: Q6G9K4, EC: 5.99.1.- | ||
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#2: Chemical | ChemComp-EDO / #3: 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: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 50 mM tris.HCl, pH 8.5, 200 mM NaCl, 12-16% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2006 / Details: mirrors |
Radiation | Monochromator: horizontally side diffracting Silicon 111 crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→88 Å / Num. all: 16226 / Num. obs: 16113 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 78.5 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2289 / Rsym value: 0.425 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AB4 Resolution: 2.8→19.64 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 35.909 / SU ML: 0.352 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 1.352 / ESU R Free: 0.393 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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