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Yorodumi- PDB-1c9s: CRYSTAL STRUCTURE OF A COMPLEX OF TRP RNA-BINDING ATTENUATION PRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c9s | ||||||
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Title | CRYSTAL STRUCTURE OF A COMPLEX OF TRP RNA-BINDING ATTENUATION PROTEIN WITH A 53-BASE SINGLE STRANDED RNA CONTAINING ELEVEN GAG TRIPLETS SEPARATED BY AU DINUCLEOTIDES | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / TRAP / PROTEIN-RNA COMPLEX / TRANSCRIPTION / SINGLE STRANDED RNA / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Antson, A.A. / Dodson, E.J. / Dodson, G.G. / Greaves, R.B. / Chen, X.-P. / Gollnick, P. | ||||||
Citation | Journal: Nature / Year: 1999 Title: Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Authors: Antson, A.A. / Dodson, E.J. / Dodson, G. / Greaves, R.B. / Chen, X. / Gollnick, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c9s.cif.gz | 368.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c9s.ent.gz | 295.2 KB | Display | PDB format |
PDBx/mmJSON format | 1c9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c9s ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c9s | HTTPS FTP |
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-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
#1: RNA chain | Mass: 18159.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IN-VITRO TRANSCRIPTION | ||||
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#2: Protein | Mass: 8257.377 Da / Num. of mol.: 22 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: PTZSTMTRB / Production host: Escherichia coli (E. coli) / Strain (production host): SG62052/PGP1-2 / References: UniProt: Q9X6J6 #3: Chemical | ChemComp-TRP / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.48 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 2000 MONOMETHYL ETHER, TRIETHANOLAMINE, MGCL2, K-GLUTAMATE, K-PHOSPHATE, L- TRYPTOPHAN, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 1544402 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.396 / % possible all: 71.7 |
Reflection | *PLUS Num. obs: 154404 |
Reflection shell | *PLUS % possible obs: 71.7 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Resolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.188 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.5 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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