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- PDB-5uj1: Crystal structure of Mycobacterium tuberculosis Topoisomerase I a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uj1 | |||||||||
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Title | Crystal structure of Mycobacterium tuberculosis Topoisomerase I at 2.15A resolution limit | |||||||||
![]() | DNA topoisomerase 1![]() | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() negative regulation of ribonuclease activity / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cao, N. / Tan, K. / Tse-Dinh, Y.C. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 287.5 KB | Display | ![]() |
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PDB format | ![]() | 230.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ujyC ![]() 6cq2C ![]() 6cqiC ![]() 5d5hS ![]() 5ukt S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() Gene: topA_1, topA, BN1213_00605, BN1303_02614, ERS013471_01645, ERS027644_01463, ERS124361_02532, RN05_3882 Plasmid: PET-HIS6-MOCR TEV-LIC / Production host: ![]() ![]() ![]() References: UniProt: A0A0E8VY41, UniProt: P9WG49*PLUS, ![]() |
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#2: Chemical | ChemComp-SO4 / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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