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Yorodumi- PDB-2be5: Crystal structure of the T. Thermophilus RNA polymerase holoenzym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2be5 | ||||||
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Title | Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin | ||||||
Components |
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Keywords | TRANSFERASE / RNA POLYMERASE HOLOENZYME / TAGETITOXIN / ANTIBIOTIC / TRANSCRIPTION REGULATION / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
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 / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Vassylyev, D.G. / Svetlov, V. / Vassylyeva, M.N. / Perederina, A. / Igarashi, N. / Matsugaki, N. / Wakatsuki, S. / Artsimovitch, I. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: Structural basis for transcription inhibition by tagetitoxin Authors: Vassylyev, D.G. / Svetlov, V. / Vassylyeva, M.N. / Perederina, A. / Igarashi, N. / Matsugaki, N. / Wakatsuki, S. / Artsimovitch, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2be5.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2be5.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 2be5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2be5_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2be5_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 2be5_validation.xml.gz | 420.7 KB | Display | |
Data in CIF | 2be5_validation.cif.gz | 609.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2be5 ftp://data.pdbj.org/pub/pdb/validation_reports/be/2be5 | HTTPS FTP |
-Related structure data
Related structure data | 1iw7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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
-DNA-directed RNA polymerase ... , 3 types, 8 molecules ABKLCMDN
#1: Protein | Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase #2: Protein | Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE9, DNA-directed RNA polymerase #3: Protein | Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE8, DNA-directed RNA polymerase |
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-RNA polymerase ... , 2 types, 4 molecules EOFP
#4: Protein | Mass: 11521.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE7 #5: Protein | Mass: 48568.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SKW1 |
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-Non-polymers , 4 types, 8194 molecules
#6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-ZN / #8: Chemical | #9: 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: 5.2 Å3/Da / Density % sol: 75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MG FORMATE, PEG400, SPERMIDINE, TRIS HCL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2004 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.4→25 Å / Num. all: 604295 / Num. obs: 604295 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.95 % / Rmerge(I) obs: 0.105 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.3 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IW7 Resolution: 2.4→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (-H,-K,L) AND THE TWINNING FRACTION IS 0.5. THE R-FACTOR IS 0.230 AND THE R-FREE IS 0.268 WHEN THIS TWINNING OPERATOR IS USED.
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Displacement parameters | Biso mean: 70.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å
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