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Yorodumi- PDB-1l9z: Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l9z | ||||||
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Title | Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / helix-turn-helix / coiled-coil / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information 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 / DNA-templated transcription / magnesium ion binding / DNA 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 / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 6.5 Å | ||||||
Authors | Murakami, K.S. / Masuda, S. / Campbell, E.A. / Muzzin, O. / Darst, S.A. | ||||||
Citation | Journal: Science / Year: 2002 Title: Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Authors: Murakami, K.S. / Masuda, S. / Campbell, E.A. / Muzzin, O. / Darst, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l9z.cif.gz | 406.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l9z.ent.gz | 180.9 KB | Display | PDB format |
PDBx/mmJSON format | 1l9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/1l9z ftp://data.pdbj.org/pub/pdb/validation_reports/l9/1l9z | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 UT
#1: DNA chain | Mass: 10801.969 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 9166.931 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-RNA POLYMERASE, ... , 4 types, 5 molecules ABCDE
#3: Protein | Mass: 34830.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU8, DNA-directed RNA polymerase #4: Protein | | Mass: 124800.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase #5: Protein | | Mass: 171187.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase #6: Protein | | Mass: 11642.423 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9EVV4, DNA-directed RNA polymerase |
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-Protein , 1 types, 1 molecules H
#7: Protein | Mass: 49922.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: rpoD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9EZJ8 |
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-Non-polymers , 2 types, 3 molecules
#8: Chemical | ChemComp-MG / |
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#9: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.78 Å3/Da / Density % sol: 74.27 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium sulfate, Tris, Magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 75 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.94799 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94799 Å / Relative weight: 1 |
Reflection | Resolution: 6.5→80 Å / Num. all: 17816 / Num. obs: 16195 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 6.5→6.73 Å / Redundancy: 2.4 % / Rsym value: 0.241 / % possible all: 78.5 |
Reflection | *PLUS Lowest resolution: 80 Å / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 78.5 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Resolution: 6.5→80 Å / Num. reflection obs: 16195 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.5→80 Å
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Refinement | *PLUS Lowest resolution: 80 Å / Rfactor obs: 0.448 / Rfactor Rfree: 0.452 / Rfactor Rwork: 0.448 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |