+Open data
-Basic information
Entry | Database: PDB / ID: 1l9u | ||||||
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Title | THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION | ||||||
Components |
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Keywords | TRANSCRIPTION / helix-turn-helix / coiled-coil | ||||||
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: 4 Å | ||||||
Authors | Murakami, K.S. / Masuda, S. / Darst, S.A. | ||||||
Citation | Journal: Science / Year: 2002 Title: Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Authors: Murakami, K.S. / Masuda, S. / 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 | 1l9u.cif.gz | 748.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l9u.ent.gz | 328.2 KB | Display | PDB format |
PDBx/mmJSON format | 1l9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l9u_validation.pdf.gz | 473.5 KB | Display | wwPDB validaton report |
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Full document | 1l9u_full_validation.pdf.gz | 643 KB | Display | |
Data in XML | 1l9u_validation.xml.gz | 101.5 KB | Display | |
Data in CIF | 1l9u_validation.cif.gz | 164.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/1l9u ftp://data.pdbj.org/pub/pdb/validation_reports/l9/1l9u | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-RNA POLYMERASE, ... , 4 types, 10 molecules ABJKCLDMEN
#1: Protein | Mass: 34830.895 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU8, DNA-directed RNA polymerase #2: Protein | Mass: 124800.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase #3: Protein | Mass: 171187.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase #4: Protein | Mass: 11642.423 Da / Num. of mol.: 2 / 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, 2 molecules HQ
#5: Protein | Mass: 38186.723 Da / Num. of mol.: 2 / Fragment: RESIDUES 92-438 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, 6 molecules
#6: Chemical | #7: Chemical | ChemComp-ZN / |
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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: 3.92 Å3/Da / Density % sol: 68.66 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: HEPES, sodium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / 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: APS / Beamline: 19-ID / Wavelength: 1.0332 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 6, 2001 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. all: 107237 / Num. obs: 85682 / % possible obs: 79.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 4→4.14 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.357 / % possible all: 70.1 |
Reflection | *PLUS Highest resolution: 4 Å / Lowest resolution: 50 Å / Num. measured all: 107237 / Rmerge(I) obs: 0.158 |
Reflection shell | *PLUS % possible obs: 70.1 % / Rmerge(I) obs: 0.357 |
-Processing
Software |
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Refinement | Highest resolution: 4 Å / Details: the coordinates contain only a CA trace. | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4 Å
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.345 / Rfactor Rfree: 0.397 / Rfactor Rwork: 0.345 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |