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Yorodumi- PDB-3mwk: Q28E mutant of HERA N-terminal RecA-like domain, complex with 8-o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mwk | ||||||
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Title | Q28E mutant of HERA N-terminal RecA-like domain, complex with 8-oxo-AMP | ||||||
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: 1.45 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 | 3mwk.cif.gz | 185.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mwk.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/3mwk ftp://data.pdbj.org/pub/pdb/validation_reports/mw/3mwk | HTTPS FTP |
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-Related structure data
Related structure data | 3mwjC 3mwlC 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 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-8OP / [( | #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: 2.55 Å3/Da / Density % sol: 51.81 % |
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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: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→46.6 Å / Num. obs: 82310 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.019 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3261 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GXS Resolution: 1.45→45.96 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.763 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.067 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.825 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→45.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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