[English] 日本語
Yorodumi- PDB-3tj1: Crystal Structure of RNA Polymerase I Transcription Initiation Fa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tj1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of RNA Polymerase I Transcription Initiation Factor Rrn3 | ||||||
Components | RNA polymerase I-specific transcription initiation factor RRN3 | ||||||
Keywords | TRANSCRIPTION / HEAT repeat / Transcription Factor / Nucleus | ||||||
Function / homology | Function and homology information RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase I promoter / nucleolus / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å | ||||||
Authors | Blattner, C. / Jennebach, S. / Herzog, F. / Mayer, A. / Cheung, A.C.M. / Witte, G. / Lorenzen, K. / Hopfner, K.-P. / Heck, A.J.R. / Aebersold, R. / Cramer, P. | ||||||
Citation | Journal: Genes Dev. / Year: 2011 Title: Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Authors: Blattner, C. / Jennebach, S. / Herzog, F. / Mayer, A. / Cheung, A.C. / Witte, G. / Lorenzen, K. / Hopfner, K.P. / Heck, A.J. / Aebersold, R. / Cramer, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tj1.cif.gz | 409 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tj1.ent.gz | 338.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tj1_validation.pdf.gz | 450 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3tj1_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 3tj1_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 3tj1_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/3tj1 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/3tj1 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 74831.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RRN3, YKL125W / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P36070 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 14% PEG 3350, 250 mM sodium-potassium-tartrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0086, 1.0094, 1.0129 | ||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2008 | ||||||||||||
Radiation | Monochromator: Liquid nitrogen cooled channel-cut silicon monochromator Si(111) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.85→50 Å / Num. all: 38079 / Num. obs: 38054 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||
Reflection shell | Resolution: 2.85→2.92 Å / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.85→48.55 Å / Cor.coef. Fo:Fc: 0.9308 / Cor.coef. Fo:Fc free: 0.9165 / SU R Cruickshank DPI: 0.701 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.5 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.436 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→48.55 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.85→2.93 Å / Total num. of bins used: 19
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|