+Open data
-Basic information
Entry | Database: PDB / ID: 4pu9 | ||||||
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Title | E. coli GyrB 43-kDa N-terminal fragment in complex with ADP-BeF3 | ||||||
Components | GyrBDNA gyrase | ||||||
Keywords | ISOMERASE / GyrB / ATP hydrolysis | ||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Stanger, F.V. / Schirmer, T. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis Authors: Stanger, F.V. / Dehio, C. / Schirmer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pu9.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pu9.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/4pu9 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/4pu9 | HTTPS FTP |
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-Related structure data
Related structure data | 4prvC 4prxC 4r1fC 1ei1S S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 44118.641 Da / Num. of mol.: 1 / Fragment: UNP residues 2-392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AES6, EC: 5.99.1.3 |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-BEF / |
#4: Chemical | ChemComp-MG / |
#5: 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: 3.05 Å3/Da / Density % sol: 59.32 % / Mosaicity: 0.461 ° |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M NaF, 0.1M Bis-Tris propane pH 6.5 and 20%(w/v) PEG3350, vapor diffusion, sitting drop, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97932 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 20, 2013 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.4→79.92 Å / Num. all: 20138 / Num. obs: 20138 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 16.6 / Scaling rejects: 5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EI1 Resolution: 2.4→44.08 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU B: 8.687 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 97.92 Å2 / Biso mean: 41.852 Å2 / Biso min: 21.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→44.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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