+Open data
-Basic information
Entry | Database: PDB / ID: 2ext | ||||||
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Title | TRAP4 (engineered TRAP) | ||||||
Components | Transcription attenuation protein mtrB | ||||||
Keywords | RNA BINDING PROTEIN / ARTIFICIAL / ENGINEERED / RING PROTEIN / 12-mer | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Heddle, J.G. / Yokoyama, T. / Yamashita, I. / Park, S.Y. / Tame, J.R.H. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Rounding up: Engineering 12-Membered Rings from the Cyclic 11-Mer TRAP Authors: Heddle, J.G. / Yokoyama, T. / Yamashita, I. / Park, S.Y. / Tame, J.R.H. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE POLYPEPTIDE CHAIN CONTAINS FOUR (4) COPIES OF THE TRAP PROTEIN LINKED IN TANDEM, WHICH ARRANGE THEMSELVES TO MAKE A 12-MER RING IN SOLUTION. THIS RING IS ALIGNED WITH THE CRYSTALLOGRAPHIC FOUR-FOLD AXIS, SO THAT ONLY THREE COPIES OF TRAP ARE PRESENT IN THE ASYMMETRIC UNIT. EACH COPY REPRESENTS A SYMMETRY AVERAGE. THE LINKER PEPTIDES ARE NOT VISIBLE IN THE ELECTRON DENSITY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ext.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ext.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ext.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/2ext ftp://data.pdbj.org/pub/pdb/validation_reports/ex/2ext | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8470.608 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: MTRB / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9X6J6 #2: Chemical | #3: 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: 2.19 Å3/Da / Density % sol: 43.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 40% PEG 200, 90mM CAPS, 200mM ammonium sulphate, pH 9.5, VAPOR DIFFUSION, HANGING 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 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 276410 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 13 |
Reflection shell | Highest resolution: 1.8 Å / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.12 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.12 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.477 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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