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Yorodumi- PDB-4wuc: N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit gr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wuc | ||||||
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Title | N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM NaCl condition | ||||||
Components | DNA gyrase subunit B | ||||||
Keywords | ISOMERASE / DNA gyrase / ATPase domain / ATPase activity / GHKL superfamily / monovalent cations | ||||||
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 strain K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Hearnshaw, S.J. / Chung, T.T. / Stevenson, C.E.M. / Maxwell, A. / Lawson, D.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: The role of monovalent cations in the ATPase reaction of DNA gyrase Authors: Hearnshaw, S.J. / Chung, T.T. / Stevenson, C.E.M. / Maxwell, A. / Lawson, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wuc.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wuc.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 4wuc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/4wuc ftp://data.pdbj.org/pub/pdb/validation_reports/wu/4wuc | HTTPS FTP |
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-Related structure data
Related structure data | 4wubC 4wudC 4xtjC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43315.766 Da / Num. of mol.: 1 / Fragment: N-terminal 43 kDa fragment, UNP residues 2-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli strain K-12 (bacteria) Gene: gyrB, acrB, himB, hisU, nalC, parA, pcbA, b3699, JW5625 Plasmid: pAJ1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P0AES6, EC: 5.99.1.3 |
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-Non-polymers , 5 types, 199 molecules
#2: Chemical | ChemComp-ANP / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: 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: 2.84 Å3/Da / Density % sol: 56.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15-25% PEG 3350, 2 mM MgCl2, 100 mM Tris-HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.033 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2012 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.9→27.49 Å / Num. obs: 39031 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Net I/σ(I): 22.4 / Num. measured all: 253416 / Scaling rejects: 3 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EI1 Resolution: 1.9→27.49 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2128 / WRfactor Rwork: 0.1788 / FOM work R set: 0.8393 / SU B: 6.32 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1285 / SU Rfree: 0.1247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 89.07 Å2 / Biso mean: 35.761 Å2 / Biso min: 21.05 Å2
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Refinement step | Cycle: final / Resolution: 1.9→27.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.903→1.952 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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