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Yorodumi- PDB-1zyr: Structure of Thermus thermophilus RNA polymerase holoenzyme in co... -
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-Basic information
Entry | Database: PDB / ID: 1zyr | ||||||
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Title | Structure of Thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin | ||||||
Components | (DNA-directed RNA polymerase ...) x 5 | ||||||
Keywords | TRANSCRIPTION / TRANSFERASE / RNA polymerase / streptolydigin / holoenzyme | ||||||
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: 3 Å | ||||||
Authors | Tuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark, A.D. ...Tuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark, A.D. / Dharia, C. / Napoli, A. / Laptenko, O. / Lee, J. / Borukhov, S. / Ebright, R.H. / Arnold, E. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2005 Title: Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Authors: Tuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark, A.D. / Dharia, C. / Napoli, A. / Laptenko, O. / Lee, J. ...Authors: Tuske, S. / Sarafianos, S.G. / Wang, X. / Hudson, B. / Sineva, E. / Mukhopadhyay, J. / Birktoft, J.J. / Leroy, O. / Ismail, S. / Clark, A.D. / Dharia, C. / Napoli, A. / Laptenko, O. / Lee, J. / Borukhov, S. / Ebright, R.H. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zyr.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1zyr.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1zyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zyr_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1zyr_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1zyr_validation.xml.gz | 311.3 KB | Display | |
Data in CIF | 1zyr_validation.cif.gz | 410.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/1zyr ftp://data.pdbj.org/pub/pdb/validation_reports/zy/1zyr | HTTPS FTP |
-Related structure data
Related structure data | 2cw0C 1iw7S 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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2 |
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Unit cell |
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-Components
-DNA-directed RNA polymerase ... , 5 types, 12 molecules ABKLCMDNEOFP
#1: Protein | Mass: 35056.164 Da / Num. of mol.: 4 / Fragment: subumit alpha / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHR6, DNA-directed RNA polymerase #2: Protein | Mass: 125436.539 Da / Num. of mol.: 2 / Fragment: subunit beta / 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 / Fragment: subunit beta-prime / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE8, DNA-directed RNA polymerase #4: Protein | Mass: 11521.221 Da / Num. of mol.: 2 / Fragment: subunit omega / 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 / Fragment: subunit sigma / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SKW1 |
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-Non-polymers , 3 types, 8 molecules
#6: Chemical | #7: Chemical | ChemComp-ZN / #8: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.85 Details: 33 mM Magnesium formate over a reservoir of 33 mM Magnesium format and 30 mM sodium citrate pH 5.85, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 139391 / Num. obs: 139391 / Observed criterion σ(I): -1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3→3.11 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IW7 Resolution: 3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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