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Yorodumi- PDB-6koq: Mycobacterium tuberculosis initial transcription complex comprisi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6koq | |||||||||
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Title | Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 10 nt | |||||||||
Components |
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Keywords | TRANSCRIPTION | |||||||||
Function / homology | Function and homology information response to nitrosative stress / 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 / cellular response to heat ...response to nitrosative stress / 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 / cellular response to heat / response to heat / response to oxidative stress / protein dimerization activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.353 Å | |||||||||
Authors | Li, L. / Zhang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. Authors: Li, L. / Molodtsov, V. / Lin, W. / Ebright, R.H. / Zhang, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6koq.cif.gz | 645.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6koq.ent.gz | 501.5 KB | Display | PDB format |
PDBx/mmJSON format | 6koq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/6koq ftp://data.pdbj.org/pub/pdb/validation_reports/ko/6koq | HTTPS FTP |
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-Related structure data
Related structure data | 6konC 6kooC 6kopC 6kqdC 6kqeC 6kqfC 6kqgC 6kqhC 6kqlC 6kqmC 6kqnC 6l74C 6ltsC 6tyeC 6tyfC 6tygC 5zx3S 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
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 40279.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: rpoA, Rv3457c, MTCY13E12.10c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGZ1, DNA-directed RNA polymerase #2: Protein | | Mass: 129602.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: rpoB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGY9, DNA-directed RNA polymerase #3: Protein | | Mass: 147068.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: rpoC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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 H37Rv (bacteria) Strain: H37Rv / Gene: rpoZ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGY5, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules GH
#6: DNA chain | Mass: 7152.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#7: DNA chain | Mass: 6535.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / RNA chain , 2 types, 2 molecules FI
#5: Protein | Mass: 24382.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: sigH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WGH9 |
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#8: RNA chain | Mass: 3096.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 24 molecules
#9: Chemical | #10: Chemical | ChemComp-MG / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.97 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.08 M magnesium acetate, 0.05 M sodium cacodylated pH 6.5, 15% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.35→50 Å / Num. obs: 64492 / % possible obs: 97.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.067 / Rrim(I) all: 0.159 / Χ2: 0.903 / Net I/σ(I): 4.6 / Num. measured all: 348311 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZX3 Resolution: 3.353→36.512 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.75 / 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: 216.1 Å2 / Biso mean: 103.0437 Å2 / Biso min: 33.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.353→36.512 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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