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- PDB-5uhf: Crystal structure of Mycobacterium tuberculosis transcription ini... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uhf | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis transcription initiation complex in complex with D-IX336 | ||||||
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![]() | TRANSCRIPTION/DNA/RNA / RNA polymerase complex / transcription / DNA / RNA / TRANSCRIPTION-DNA-RNA complex | ||||||
Function / homology | ![]() response to water / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity ...response to water / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lin, W. / Das, K. / Feng, Y. / Ebright, R.H. | ||||||
![]() | ![]() Title: Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition. Authors: Lin, W. / Mandal, S. / Degen, D. / Liu, Y. / Ebright, Y.W. / Li, S. / Feng, Y. / Zhang, Y. / Mandal, S. / Jiang, Y. / Liu, S. / Gigliotti, M. / Talaue, M. / Connell, N. / Das, K. / Arnold, E. / Ebright, R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 665.3 KB | Display | ![]() |
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PDB format | ![]() | 537.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 698.6 KB | Display | ![]() |
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Full document | ![]() | 739.1 KB | Display | |
Data in XML | ![]() | 63.8 KB | Display | |
Data in CIF | ![]() | 96.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uh5C ![]() 5uh6C ![]() 5uh7C ![]() 5uh8C ![]() 5uh9C ![]() 5uhaC ![]() 5uhbC ![]() 5uhcC ![]() 5uhdC ![]() 5uheC ![]() 5uhgC 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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Unit cell |
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 37745.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: rpoA, Rv3457c, MTCY13E12.10c Production host: ![]() ![]() References: UniProt: P9WGZ1, DNA-directed RNA polymerase #2: Protein | | Mass: 130018.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: rpoB, Rv0667, MTCI376.08c Production host: ![]() ![]() References: UniProt: P9WGY9, DNA-directed RNA polymerase #3: Protein | | Mass: 146968.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: rpoC, Rv0668, MTCI376.07c Production host: ![]() ![]() References: UniProt: P9WGY7, DNA-directed RNA polymerase #4: Protein | | Mass: 11851.140 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: rpoZ, Rv1390, MTCY21B4.07 Production host: ![]() ![]() References: UniProt: P9WGY5, DNA-directed RNA polymerase |
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-Protein , 1 types, 1 molecules F
#5: Protein | Mass: 57877.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: sigA, mysA, rpoD, rpoV, Rv2703, MTCY05A6.24 Production host: ![]() ![]() References: UniProt: P9WGI1 |
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-DNA chain , 2 types, 2 molecules HG
#6: DNA chain | Mass: 7160.632 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
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#7: DNA chain | Mass: 4899.180 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
-Non-polymers , 3 types, 4 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/88D.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/88D.gif)
#8: Chemical | #9: Chemical | ChemComp-MG / | #10: Chemical | ChemComp-88D / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 50 mM Tris-HCl, pH 8.4, 200 mM KCl, 50 mM MgCl2, and 10% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.35→50 Å / Num. obs: 44904 / % possible obs: 99 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.065 / Rrim(I) all: 0.212 / Χ2: 0.945 / Net I/σ(I): 4.8 / Num. measured all: 395911 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 4.345→48.504 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 373.71 Å2 / Biso mean: 68.0678 Å2 / Biso min: 19.09 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.345→48.504 Å
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