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Yorodumi- PDB-5uh5: Crystal structure of Mycobacterium tuberculosis transcription ini... -
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-Basic information
Entry | Database: PDB / ID: 5uh5 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis transcription initiation complex containing 3 nt of RNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA/RNA / RNA polymerase complex / transcription / DNA / RNA / TRANSCRIPTION-DNA-RNA complex | ||||||
Function / homology | Function and homology information response to water / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / 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 / peptidoglycan-based cell wall / DNA-directed RNA polymerase complex / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.746 Å | ||||||
Authors | Lin, W. / Das, K. / Feng, Y. / Ebright, R.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol. Cell / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uh5.cif.gz | 673.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uh5.ent.gz | 530.4 KB | Display | PDB format |
PDBx/mmJSON format | 5uh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/5uh5 ftp://data.pdbj.org/pub/pdb/validation_reports/uh/5uh5 | HTTPS FTP |
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-Related structure data
Related structure data | 5uh6C 5uh7C 5uh8C 5uh9C 5uhaC 5uhbC 5uhcC 5uhdC 5uheC 5uhfC 5uhgC 4g7hS 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
-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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoA, Rv3457c, MTCY13E12.10c / Production host: Escherichia coli (E. coli) / 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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoB, Rv0667, MTCI376.08c / Production host: Escherichia coli (E. coli) / 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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoC, Rv0668, MTCI376.07c / Production host: Escherichia coli (E. coli) / 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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoZ, Rv1390, MTCY21B4.07 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGY5, DNA-directed RNA polymerase |
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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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) |
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#7: DNA chain | Mass: 4899.180 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) |
-Protein / RNA chain , 2 types, 2 molecules FI
#5: Protein | Mass: 57877.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: sigA, mysA, rpoD, rpoV, Rv2703, MTCY05A6.24 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGI1 |
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#8: RNA chain | Mass: 974.660 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) |
-Non-polymers , 2 types, 3 molecules
#9: Chemical | #10: Chemical | ChemComp-MG / | |
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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: 2.76 Å3/Da / Density % sol: 55.49 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 400 ul 50 mM Tris-HCl, pH 8.2, 200 mM KCl, 50 mM MgCl2, and 10% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03316 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Mar 9, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03316 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.75→50 Å / Num. obs: 50207 / % possible obs: 99.7 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.055 / Rrim(I) all: 0.184 / Χ2: 0.973 / Net I/σ(I): 4.4 / Num. measured all: 522522 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G7H Resolution: 3.746→49.6 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 20.89 / 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: 189.25 Å2 / Biso mean: 49.9733 Å2 / Biso min: 0 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.746→49.6 Å
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