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Yorodumi- PDB-3m4i: Crystal structure of the second part of the Mycobacterium tubercu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m4i | ||||||
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Title | Crystal structure of the second part of the Mycobacterium tuberculosis DNA gyrase reaction core: the TOPRIM domain at 1.95 A resolution | ||||||
Components | DNA gyrase subunit B | ||||||
Keywords | ISOMERASE / DNA GYRASE / GYRB / TOPRIM / TYPE II TOPOISOMERASE / TUBERCULOSIS / QUINOLONE BINDING SITE / DNA BINDING SITE / ATP-BINDING / NUCLEOTIDE-BINDING / TOPOISOMERASE | ||||||
Function / homology | Function and homology information DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / DNA binding ...DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / DNA binding / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Piton, J. / Petrella, S. / Aubry, A. / Mayer, C. | ||||||
Citation | Journal: Plos One / Year: 2010 Title: Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase. Authors: Piton, J. / Petrella, S. / Delarue, M. / Andre-Leroux, G. / Jarlier, V. / Aubry, A. / Mayer, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m4i.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m4i.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 3m4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m4i_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
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Full document | 3m4i_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 3m4i_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 3m4i_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/3m4i ftp://data.pdbj.org/pub/pdb/validation_reports/m4/3m4i | HTTPS FTP |
-Related structure data
Related structure data | 3ifzC 3ig0C 1ab4S 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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Unit cell |
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-Components
#1: Protein | Mass: 27419.260 Da / Num. of mol.: 1 / Fragment: TOPRIM DOMAIN (C-TERMINAL DOMAIN) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: HR37RV / Gene: gyrB, MT0005, MTCY10H4.03, Rv0005 / Plasmid: PRSF-2 EK/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA 2 References: UniProt: P0C5C5, UniProt: P9WG45*PLUS, EC: 5.99.1.3 |
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#2: Chemical | ChemComp-MPD / ( |
#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: 2.42 Å3/Da / Density % sol: 49.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: AMMONIUM SULFATE, TRIS, PEG 4000, CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2010 Details: KIRKPATRICK-BAEZ PAIR OF BIMORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL |
Radiation | Monochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→29.39 Å / Num. all: 20688 / Num. obs: 20626 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.08 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2913 / Rsym value: 0.629 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AB4 Resolution: 1.95→17 Å / Cor.coef. Fo:Fc: 0.9372 / Cor.coef. Fo:Fc free: 0.9277 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.126
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Displacement parameters | Biso mean: 39.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.291 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.06 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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