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Yorodumi- PDB-5w7n: 2-Se-T2/4-DNA and native RNA hybrid in complex with RNase H catal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w7n | ||||||
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Title | 2-Se-T2/4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant | ||||||
Components |
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Keywords | HYDROLASE/DNA/RNA / HYDROLASE-DNA-RNA complex | ||||||
Function / homology | Function and homology information ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fang, Z. / Yang, F. / Huang, Z. | ||||||
Citation | Journal: To Be Published Title: 2-Se-T2/4-modified-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant Authors: Fang, Z. / Yang, F. / Huang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w7n.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w7n.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 5w7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/5w7n ftp://data.pdbj.org/pub/pdb/validation_reports/w7/5w7n | HTTPS FTP |
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-Related structure data
Related structure data | 2g8uS S: Starting model for refinement |
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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: RNA chain | Mass: 1875.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: DNA chain | Mass: 1950.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Protein | Mass: 15243.206 Da / Num. of mol.: 1 / Fragment: residues 62-193 / Mutation: D132N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria) Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 Gene: rnhA, BH0863 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9KEI9, ribonuclease H | ||
#4: Chemical | #5: 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: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 12%(w/v) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→61.85 Å / Num. obs: 17561 / % possible obs: 88.9 % / Redundancy: 4.3 % / Rpim(I) all: 0.027 / Χ2: 0.784 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 5.3 / Num. unique obs: 913 / CC1/2: 0.974 / Rpim(I) all: 0.085 / Χ2: 0.784 / % possible all: 52.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2g8u Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.68 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.24 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→50 Å
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Refine LS restraints |
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