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Yorodumi- PDB-6dvd: Crystal structure of Mycobacterium tuberculosis transcription ini... -
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-Basic information
Entry | Database: PDB / ID: 6dvd | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) with 6 nt spacer and bromine labelled in position "-11 | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Mycobacterium tuberculosis / RNA polymerase / ECF sigma factor / TRANSFERASE / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information 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 ...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 / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.899 Å | ||||||
Authors | Lin, W. / Das, K. / Feng, Y. / Ebright, R.H. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis of ECF-sigma-factor-dependent transcription initiation. Authors: Lin, W. / Mandal, S. / Degen, D. / Cho, M.S. / Feng, Y. / Das, K. / 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 | 6dvd.cif.gz | 638.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dvd.ent.gz | 504.1 KB | Display | PDB format |
PDBx/mmJSON format | 6dvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/6dvd ftp://data.pdbj.org/pub/pdb/validation_reports/dv/6dvd | HTTPS FTP |
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-Related 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: 39315.027 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 'BL21-Gold(DE3)pLysS AG' (bacteria) 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 'BL21-Gold(DE3)pLysS AG' (bacteria) 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 'BL21-Gold(DE3)pLysS AG' (bacteria) 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 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WGY5, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules GH
#6: DNA chain | Mass: 3045.005 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
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#7: DNA chain | Mass: 7401.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
-Protein / Non-polymers , 2 types, 3 molecules F
#5: Protein | Mass: 19563.074 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: sigL, Rv0735 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WGH5 |
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#8: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 100 mM sodium citrate tribasic dihydrate, pH 6.2, 200 mM sodium acetate, and 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→50 Å / Num. obs: 44608 / % possible obs: 87.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 3.9→3.97 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.768 / % possible all: 68.5 |
-Processing
Software |
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Refinement | Resolution: 3.899→45.899 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.12 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.899→45.899 Å
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Refine LS restraints |
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LS refinement shell |
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