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Yorodumi- PDB-3mwl: Q28E mutant of HERA N-terminal RecA-like domain in complex with 8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mwl | ||||||
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Title | Q28E mutant of HERA N-terminal RecA-like domain in complex with 8-OXOADENOSINE | ||||||
Components | Heat resistant RNA dependent ATPase | ||||||
Keywords | HYDROLASE / RNA HELICASE / RIBOSOME BIOGENESIS / THERMOPHILIC / ATPASE | ||||||
Function / homology | Function and homology information nucleic acid binding / RNA helicase activity / hydrolase activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Rudolph, M.G. / Klostermeier, D. | ||||||
Citation | Journal: Biol.Chem. / Year: 2011 Title: Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop. Authors: Strohmeier, J. / Hertel, I. / Diederichsen, U. / Rudolph, M.G. / Klostermeier, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mwl.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mwl.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 3mwl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/3mwl ftp://data.pdbj.org/pub/pdb/validation_reports/mw/3mwl | HTTPS FTP |
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-Related structure data
Related structure data | 3mwjC 3mwkC 3nbfC 3nejC 2gxsS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22343.938 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: Q28E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_C1895 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72GF3 #2: Chemical | #3: Chemical | ChemComp-8OX / | #4: 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: 2.59 Å3/Da / Density % sol: 52.51 % |
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Crystal grow | Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.906 Å / Num. obs: 60859 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1582 / % possible all: 70.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GXS Resolution: 1.6→46.906 Å / SU ML: 0.21 / σ(F): 0.02 / Phase error: 25.21 / 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: 48.363 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→46.906 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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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