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Yorodumi- PDB-5tw1: Crystal structure of a Mycobacterium smegmatis transcription init... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tw1 | ||||||
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Title | Crystal structure of a Mycobacterium smegmatis transcription initiation complex with RbpA | ||||||
Components |
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Keywords | TRANSCRIPTION ACTIVATOR/TRANSFERASE/DNA / TRANSCRIPTION ACTIVATOR-TRANSFERASE-DNA 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) Mycobacterium smegmatis str. MC2 155 (bacteria) Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Hubin, E.A. / Darst, S.A. / Campbell, E.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2017 Title: Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. Authors: Hubin, E.A. / Fay, A. / Xu, C. / Bean, J.M. / Saecker, R.M. / Glickman, M.S. / 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 | 5tw1.cif.gz | 708.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tw1.ent.gz | 546.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tw1_validation.pdf.gz | 588.7 KB | Display | wwPDB validaton report |
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Full document | 5tw1_full_validation.pdf.gz | 770.9 KB | Display | |
Data in XML | 5tw1_validation.xml.gz | 135.4 KB | Display | |
Data in CIF | 5tw1_validation.cif.gz | 181.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/5tw1 ftp://data.pdbj.org/pub/pdb/validation_reports/tw/5tw1 | HTTPS FTP |
-Related structure data
Related structure data | 4xlpS 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
-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: rpoD, sigA, MSMEG_2758, MSMEI_2690 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QW02 |
-DNA-directed RNA polymerase subunit ... , 4 types, 6 molecules ABTCDE
#2: Protein | Mass: 37959.441 Da / Num. of mol.: 3 / 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: 128680.141 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 #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.) Aquifex aeolicus (bacteria) |
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#8: DNA chain | Mass: 7930.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aquifex aeolicus (bacteria) |
-Protein/peptide , 1 types, 1 molecules G
#9: Protein/peptide | Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) |
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-Non-polymers , 5 types, 146 molecules
#10: Chemical | ChemComp-SO4 / #11: Chemical | ChemComp-EDO / #12: Chemical | #13: Chemical | ChemComp-MG / | #14: 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: 2.94 Å3/Da / Density % sol: 58.22 % |
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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 LiSO4, 16% (w/v) polyetheylene 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: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→60 Å / Num. obs: 143776 / % possible obs: 99 % / Redundancy: 16.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2343 / Net I/σ(I): 22.39 |
Reflection shell | Resolution: 2.76→2.859 Å / Redundancy: 12.3 % / Rmerge(I) obs: 4.816 / Mean I/σ(I) obs: 0.77 / CC1/2: 0.214 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XLP Resolution: 2.76→54.905 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→54.905 Å
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Refine LS restraints |
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LS refinement shell |
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