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Yorodumi- PDB-3ear: Novel dimerization motif in the DEAD box RNA helicase Hera: form ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ear | ||||||
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Title | Novel dimerization motif in the DEAD box RNA helicase Hera: form 1, partial dimer | ||||||
Components | Hera | ||||||
Keywords | HYDROLASE / DEAD box RNA helicase / dimer / ATP-binding / Helicase / Nucleotide-binding | ||||||
Function / homology | Function and homology information nucleic acid binding / RNA helicase activity / hydrolase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Klostermeier, D. / Rudolph, M.G. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2009 Title: A novel dimerization motif in the C-terminal domain of the Thermus thermophilus DEAD box helicase Hera confers substantial flexibility. Authors: Klostermeier, D. / Rudolph, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ear.cif.gz | 117.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ear.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ear.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/3ear ftp://data.pdbj.org/pub/pdb/validation_reports/ea/3ear | HTTPS FTP |
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-Related structure data
Related structure data | 3eaqSC 3easC 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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Unit cell |
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-Components
#1: Protein | Mass: 23867.275 Da / Num. of mol.: 2 / Fragment: internal fragment (UNP residues 215 to 426) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_C1895 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q72GF3 #2: 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: 2.71 Å3/Da / Density % sol: 54.58 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 31, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46 Å / Num. obs: 23978 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.048 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1375 / Rsym value: 0.661 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3eaq Resolution: 2.3→45.928 Å / SU ML: 0.34 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.432 Å2 / ksol: 0.324 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45.928 Å
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Refine LS restraints |
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LS refinement shell |
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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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