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Yorodumi- PDB-4ibn: Crystal structure of LC9-RNase H1, a type 1 RNase H with the type... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ibn | ||||||
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Title | Crystal structure of LC9-RNase H1, a type 1 RNase H with the type 2 active-site motif | ||||||
Components | Ribonuclease H | ||||||
Keywords | HYDROLASE / RNase H / Ribonuclease H / Hydrolase' | ||||||
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 / molecular replacement / Resolution: 1.62 Å | ||||||
Authors | Nguyen, T.-N. / You, D.-J. / Kanaya, E. / Koga, Y. / Kanaya, S. | ||||||
Citation | Journal: Febs Lett. / Year: 2013 Title: Crystal structure of metagenome-derived LC9-RNase H1 with atypical DEDN active site motif Authors: Nguyen, T.-N. / You, D.-J. / Kanaya, E. / Koga, Y. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ibn.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ibn.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ibn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ibn_validation.pdf.gz | 426.5 KB | Display | wwPDB validaton report |
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Full document | 4ibn_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 4ibn_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 4ibn_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/4ibn ftp://data.pdbj.org/pub/pdb/validation_reports/ib/4ibn | HTTPS FTP |
-Related structure data
Related structure data | 2ehgS 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: Protein | Mass: 23832.584 Da / Num. of mol.: 1 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: E0X765, ribonuclease H |
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#2: 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: 1.71 Å3/Da / Density % sol: 28.05 % / Mosaicity: 0.962 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100mM Tris-HCl, 200mM MgCl2.6H2O, 30% PEG 4000, pH 8.5, 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: BRUKER SMART 6500 / Detector: CCD / Date: Jun 9, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: horizontal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→50 Å / Num. obs: 20537 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Χ2: 0.993 / Net I/σ(I): 43.648 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EHG Resolution: 1.62→49.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2203 / WRfactor Rwork: 0.1814 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8556 / SU B: 1.881 / SU ML: 0.067 / SU R Cruickshank DPI: 0.1101 / SU Rfree: 0.1069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 69.29 Å2 / Biso mean: 25.5324 Å2 / Biso min: 13.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→49.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.621→1.663 Å / Total num. of bins used: 20
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