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Yorodumi- PDB-4ckl: Structure of 55 kDa N-terminal domain of E. coli DNA gyrase A sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ckl | ||||||
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Title | Structure of 55 kDa N-terminal domain of E. coli DNA gyrase A subunit with simocyclinone D8 bound | ||||||
Components | DNA GYRASE SUBUNIT A | ||||||
Keywords | ISOMERASE / TOPOISOMERASE / ANTIBIOTIC TARGET | ||||||
Function / homology | Function and homology information DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Hearnshaw, S.J. / Edwards, M.J. / Stevenson, C.E.M. / Lawson, D.M. / Maxwell, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: A New Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8 Bound to DNA Gyrase Gives Fresh Insight Into the Mechanism of Inhibition. Authors: Hearnshaw, S.J. / Edwards, M.J. / Stevenson, C.E. / Lawson, D.M. / Maxwell, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ckl.cif.gz | 360.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ckl.ent.gz | 294.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ckl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ckl_validation.pdf.gz | 675.2 KB | Display | wwPDB validaton report |
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Full document | 4ckl_full_validation.pdf.gz | 688.7 KB | Display | |
Data in XML | 4ckl_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 4ckl_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/4ckl ftp://data.pdbj.org/pub/pdb/validation_reports/ck/4ckl | HTTPS FTP |
-Related structure data
Related structure data | 4ckkSC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 55381.398 Da / Num. of mol.: 2 / Fragment: 55 KDA N-TERMINAL DOMAIN, RESIDUES 30-522 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: JMTACA / Plasmid: PRJR10.18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B843 / Variant (production host): PLYSS References: UniProt: P0AES5, UniProt: A0A0H3JH39*PLUS, EC: 5.99.1.3 #2: Chemical | ChemComp-SM8 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.8 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→41.51 Å / Num. obs: 77820 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CKK Resolution: 2.05→41.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.133 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.146 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→41.51 Å
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Refine LS restraints |
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