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Yorodumi- PDB-4e19: Crystal structure of RNase H1 from halophilic archaeon Halobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+19 | ||||||
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Title | Crystal structure of RNase H1 from halophilic archaeon Halobacterium salinarum NRC-1 | ||||||
Components | ribonuclease H1 | ||||||
Keywords | HYDROLASE / RNase H1 | ||||||
Function / homology | Function and homology information exonuclease activity / ribonuclease H / RNA-DNA hybrid ribonuclease activity / DNA binding / RNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Halobacterium salinarium (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 Å | ||||||
Authors | You, D.J. / Angkawidjaja, C. / Koga, Y. / Kanaya, S. | ||||||
Citation | Journal: To be Published Title: Crystal structure of RNase H1 from halophilic archaeon Halobacterium salinarum NRC-1 Authors: You, D.J. / Angkawidjaja, C. / 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 | 4e19.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e19.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 4e19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e19_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 4e19_full_validation.pdf.gz | 436.8 KB | Display | |
Data in XML | 4e19_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 4e19_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/4e19 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/4e19 | HTTPS FTP |
-Related structure data
Related structure data | 4nynC 2ehgS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21001.799 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarium (Halophile) / Strain: NRC-1 / Gene: VNG_0255C / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9HSF6, ribonuclease H #2: Chemical | ChemComp-MN / #3: 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: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20%(W/V) PEG 8000, Imidazole(pH6.5), 3%(V/V) MPD, 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: Oct 10, 2011 |
Diffraction measurement | Details: 1.00 degrees, 0.7 sec, detector distance 150.00 mm / Method: \w scans |
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 | Av R equivalents: 0.074 / Number: 362644 |
Reflection | Resolution: 1.41→50 Å / Num. obs: 48997 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 31.61 |
Reflection shell | Resolution: 1.41→1.43 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.613 / Rsym value: 0.381 / % possible all: 98.9 |
Cell measurement | Reflection used: 362644 |
-Phasing
Phasing | Method: molecular replacement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MR |
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 41564 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EHG Resolution: 1.41→40.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 1 / SU B: 0.907 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.066 / 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: 61.16 Å2 / Biso mean: 18.1282 Å2 / Biso min: 8.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→40.94 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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