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Yorodumi- PDB-5uj1: Crystal structure of Mycobacterium tuberculosis Topoisomerase I a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uj1 | |||||||||
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Title | Crystal structure of Mycobacterium tuberculosis Topoisomerase I at 2.15A resolution limit | |||||||||
Components | DNA topoisomerase 1 | |||||||||
Keywords | ISOMERASE / Topoisomerase I / Mycobacterium tuberculosis | |||||||||
Function / homology | Function and homology information negative regulation of ribonuclease activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / peptidoglycan-based cell wall / magnesium ion binding / DNA binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å | |||||||||
Authors | Cao, N. / Tan, K. / Tse-Dinh, Y.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site. Authors: Cao, N. / Tan, K. / Annamalai, T. / Joachimiak, A. / Tse-Dinh, Y.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uj1.cif.gz | 287.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uj1.ent.gz | 230.1 KB | Display | PDB format |
PDBx/mmJSON format | 5uj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uj1_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 5uj1_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 5uj1_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 5uj1_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/5uj1 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/5uj1 | HTTPS FTP |
-Related structure data
Related structure data | 5ujyC 6cq2C 6cqiC 5d5hS 5ukt 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: 77843.500 Da / Num. of mol.: 1 / Fragment: UNP residues 63-768 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: topA_1, topA, BN1213_00605, BN1303_02614, ERS013471_01645, ERS027644_01463, ERS124361_02532, RN05_3882 Plasmid: PET-HIS6-MOCR TEV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): T7 EXPRESS CRYSTAL References: UniProt: A0A0E8VY41, UniProt: P9WG49*PLUS, DNA topoisomerase |
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#2: Chemical | ChemComp-SO4 / |
#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: 2.69 Å3/Da / Density % sol: 54.36 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M Potassium sodium tartrate, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2016 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→47.233 Å / Num. obs: 46076 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.044 / Χ2: 0.791 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.15→2.18 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2263 / CC1/2: 0.734 / Rpim(I) all: 0.391 / Χ2: 0.636 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D5H Resolution: 2.153→47.233 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.153→47.233 Å
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Refine LS restraints |
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LS refinement shell |
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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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