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Yorodumi- PDB-5vi5: Structure of Mycobacterium smegmatis transcription initiation com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vi5 | ||||||
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Title | Structure of Mycobacterium smegmatis transcription initiation complex with a full transcription bubble | ||||||
Components |
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Keywords | TRANSCRIPTION / DNA-dependent RNA polymerase / nucleotidyl transferase / transcriptioni initiation complex | ||||||
Function / homology | Function and homology information bacterial-type RNA polymerase core enzyme binding / sigma factor activity / 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 ...bacterial-type RNA polymerase core enzyme binding / sigma factor activity / 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 / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.196 Å | ||||||
Authors | Darst, S.A. / Campbell, E.A. / Lilic, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. Authors: Hubin, E.A. / Lilic, M. / Darst, S.A. / Campbell, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vi5.cif.gz | 708 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vi5.ent.gz | 545.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/5vi5 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5vi5 | HTTPS FTP |
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-Related structure data
Related structure data | 5vi8C 5tw1S 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 chain , 2 types, 2 molecules OP
#1: DNA chain | Mass: 15521.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 15393.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 1 types, 1 molecules Q
#3: RNA chain | Mass: 1240.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#4: Protein | Mass: 37959.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL8, DNA-directed RNA polymerase #5: Protein | | Mass: 128666.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: P60281, DNA-directed RNA polymerase #6: Protein | | Mass: 146756.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS66, DNA-directed RNA polymerase #7: Protein | | Mass: 11544.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QWT1, DNA-directed RNA polymerase |
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-Protein , 2 types, 2 molecules FJ
#8: Protein | Mass: 51573.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: rpoD, sigA, MSMEG_2758, MSMEI_2690 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QW02 |
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#9: Protein | Mass: 13078.731 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: rbpA, MSMEG_3858, MSMEI_3768 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QZ11 |
-Non-polymers , 4 types, 12 molecules
#10: Chemical | ChemComp-SO4 / #11: Chemical | #12: Chemical | #13: Water | ChemComp-HOH / | |
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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: 3.13 Å3/Da / Density % sol: 60.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Bis-Tris, pH 6.0, 0.2 M Lithium sulfate, 16% (w/v) polyethylene glycol 3350, 2.5% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 3.196→50.015 Å / Num. obs: 88065 / % possible obs: 95.1 % / Redundancy: 3.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.141 / Net I/σ(I): 7.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TW1 Resolution: 3.196→50.015 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33 / 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: 3.196→50.015 Å
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Refine LS restraints |
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LS refinement shell |
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