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Yorodumi- PDB-3nfi: Crystal structure of tandem winged helix domain of RNA polymerase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nfi | ||||||
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Title | Crystal structure of tandem winged helix domain of RNA polymerase I subunit A49 | ||||||
Components | DNA-directed RNA polymerase I subunit RPA49Polymerase | ||||||
Keywords | DNA BINDING PROTEIN / TRANSCRIPTION / winged helix / RNA polymerase / DNA binding | ||||||
Function / homology | Function and homology information RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / RNA polymerase I activity / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase I complex ...RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / RNA polymerase I activity / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase I complex / transcription by RNA polymerase I / ribosome biogenesis / nucleolus / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Geiger, S.R. / Lorenzen, K. / Schreieck, A. / Hanecker, P. / Kostrewa, D. / Heck, A.J.R. / Cramer, P. | ||||||
Citation | Journal: Mol.Cell / Year: 2010 Title: RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex. Authors: Geiger, S.R. / Lorenzen, K. / Schreieck, A. / Hanecker, P. / Kostrewa, D. / Heck, A.J. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nfi.cif.gz | 456.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nfi.ent.gz | 393.8 KB | Display | PDB format |
PDBx/mmJSON format | 3nfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/3nfi ftp://data.pdbj.org/pub/pdb/validation_reports/nf/3nfi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 27141.715 Da / Num. of mol.: 5 / Fragment: UNP residues 171-403 / Mutation: L178M, L261M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: N0880, RPA49, RRN13, YNL248C / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 (DE) RIL / References: UniProt: Q01080, DNA-directed RNA polymerase #2: Chemical | ChemComp-PE4 / | #3: Water | ChemComp-HOH / | Nonpolymer details | PE4 E 1 IS PEG 4000 fragment | |
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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: 2.29 Å3/Da / Density % sol: 46.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 24% PEG 3350, 50 mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 70 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9790, 0.9790, 0.9180 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2009 / Details: torodial focusing mirror | |||||||||
Radiation | Monochromator: channel cut ESRF monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→80 Å / Num. all: 95580 / Num. obs: 94313 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 31.04 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.78 | |||||||||
Reflection shell | Resolution: 1.9→2.08 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.606 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→27.82 Å / Cor.coef. Fo:Fc: 0.9527 / Cor.coef. Fo:Fc free: 0.9345 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.262 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→27.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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