+Open data
-Basic information
Entry | Database: PDB / ID: 4url | ||||||
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Title | Crystal Structure of Staph ParE43kDa in complex with KBD | ||||||
Components | DNA TOPOISOMERASE IV, B SUBUNIT | ||||||
Keywords | ISOMERASE / ANTIBIOTICS / NATURAL PRODUCT / KIBDELOMYCIN / GYRASE / TOPOISOMERASE IV | ||||||
Function / homology | Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 2-Layer Sandwich / Alpha Beta / Chem-XAM / : Function and homology information | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Lu, J. / Patel, S. / Sharma, N. / Soisson, S. / Kishii, R. / Takei, M. / Fukuda, Y. / Lumb, K.J. / Singh, S.B. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: Structures of Kibdelomycin Bound to Staphylococcus Aureus Gyrb and Pare Showed a Novel U-Shaped Binding Mode. Authors: Lu, J. / Patel, S. / Sharma, N. / Soisson, S.M. / Kishii, R. / Takei, M. / Fukuda, Y. / Lumb, K.J. / Singh, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4url.cif.gz | 153.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4url.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 4url.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/4url ftp://data.pdbj.org/pub/pdb/validation_reports/ur/4url | HTTPS FTP |
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-Related structure data
Related structure data | 4urmC 4urnC 4uroC 1s16S C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44987.363 Da / Num. of mol.: 2 / Fragment: 43KDA N-TERMINAL DOMAIN, RESIDUES 1-406 Source method: isolated from a genetically manipulated source Details: KIBDELOMYCIN / Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: X5EN43, EC: 5.99.1.- #2: Chemical | #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: 2.66 Å3/Da / Density % sol: 53.71 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.2M AMMONIUM SULFATE, 0.1M TRIS PH 8.5 AND 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 41758 / % possible obs: 99.9 % / Observed criterion σ(I): 2.7 / Redundancy: 4 % / Biso Wilson estimate: 52.27 Å2 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 20.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1S16 Resolution: 2.29→49.73 Å / Cor.coef. Fo:Fc: 0.9244 / Cor.coef. Fo:Fc free: 0.9004 / SU R Cruickshank DPI: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.215
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Displacement parameters | Biso mean: 53.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.348 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→49.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.35 Å / Total num. of bins used: 20
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