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Yorodumi- PDB-3u3g: Structure of LC11-RNase H1 Isolated from Compost by Metagenomic A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u3g | ||||||
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Title | Structure of LC11-RNase H1 Isolated from Compost by Metagenomic Approach: Insight into the Structural Bases for Unusual Enzymatic Properties of Sto-RNase H1 | ||||||
Components | Ribonuclease H | ||||||
Keywords | HYDROLASE / Cleave the RNA strand of RNA/DNA hybrid | ||||||
Function / homology | Function and homology information ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding Similarity search - Function | ||||||
Biological species | uncultured organism (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Nguyen, T.N. / Angkawidjaja, C. / Kanaya, E. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Activity, stability, and structure of metagenome-derived LC11-RNase H1, a homolog of Sulfolobus tokodaii RNase H1 Authors: Nguyen, T.N. / Angkawidjaja, C. / Kanaya, E. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u3g.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u3g.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 3u3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/3u3g ftp://data.pdbj.org/pub/pdb/validation_reports/u3/3u3g | HTTPS FTP |
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-Related structure data
Related structure data | 3h08S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15631.940 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured organism (environmental samples) Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): MIC2067(DE3) / References: UniProt: E0X767, ribonuclease H #2: Chemical | #3: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #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: 2.44 Å3/Da / Density % sol: 49.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M imidazole, 0.2M sodium cloride, 0.4M sodium dihydrogen phosphate, 1.6M dipotassium phosphate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2010 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 115103 / % possible obs: 97.4 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Rsym value: 0.051 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5082 / Rsym value: 0.422 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H08 Resolution: 1.4→47.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.885 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R Free: 0.061 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.186 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→47.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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