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Yorodumi- PDB-6dcf: Crystal structure of a Mycobacterium smegmatis transcription init... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dcf | ||||||
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Title | Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase and bound to kanglemycin A | ||||||
Components |
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Keywords | transcription/dna/antibiotic / Inhibitor / complex / RNA polymerase / transcription-dna-antibiotic 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: 3.45 Å | ||||||
Authors | Lilic, M. / Darst, S.A. / Campbell, E.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism. Authors: Peek, J. / Lilic, M. / Montiel, D. / Milshteyn, A. / Woodworth, I. / Biggins, J.B. / Ternei, M.A. / Calle, P.Y. / Danziger, M. / Warrier, T. / Saito, K. / Braffman, N. / Fay, A. / Glickman, ...Authors: Peek, J. / Lilic, M. / Montiel, D. / Milshteyn, A. / Woodworth, I. / Biggins, J.B. / Ternei, M.A. / Calle, P.Y. / Danziger, M. / Warrier, T. / Saito, K. / Braffman, N. / Fay, A. / Glickman, M.S. / Darst, S.A. / Campbell, E.A. / Brady, S.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dcf.cif.gz | 630 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dcf.ent.gz | 481.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dcf_validation.pdf.gz | 959 KB | Display | wwPDB validaton report |
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Full document | 6dcf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6dcf_validation.xml.gz | 107.6 KB | Display | |
Data in CIF | 6dcf_validation.cif.gz | 143.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/6dcf ftp://data.pdbj.org/pub/pdb/validation_reports/dc/6dcf | HTTPS FTP |
-Related structure data
Related structure data | 6cceSC 6ccvC 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
-Protein , 2 types, 2 molecules JF
#1: 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 |
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#6: 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: sigA, MSMEG_2758 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QW02 |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#2: 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 #3: Protein | | Mass: 128706.219 Da / Num. of mol.: 1 / Mutation: S447L 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: rpoB, MSMEG_1367, MSMEI_1328 / Production host: Escherichia coli (E. coli) / References: UniProt: P60281, DNA-directed RNA polymerase #4: Protein | | Mass: 146712.891 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 #5: 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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-DNA chain , 2 types, 2 molecules OP
#7: DNA chain | Mass: 9565.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#8: DNA chain | Mass: 7930.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 7 types, 23 molecules
#9: Chemical | ChemComp-KNG / | ||||||||||
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#10: Chemical | ChemComp-SO4 / #11: Chemical | #12: Chemical | ChemComp-MG / | #13: Chemical | ChemComp-GLU / | #14: Chemical | #15: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Bis-Tris, pH 6.0, 0.2 M Li-sulfate, 20% (w/v) PEG 3350, 2.5% (v/v) ethylene glycol, 1% (v/v) DMSO |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→45 Å / Num. obs: 68062 / % possible obs: 97.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 103.8 Å2 / Rmerge(I) obs: 0.162 / Net I/σ(I): 8.02 |
Reflection shell | Resolution: 3.45→3.57 Å / Redundancy: 4 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 0.67 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CCE Resolution: 3.45→43.89 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.55 / 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: 3.45→43.89 Å
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Refine LS restraints |
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LS refinement shell |
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