+Open data
-Basic information
Entry | Database: PDB / ID: 3aa5 | ||||||
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Title | A52F E.coli RNase HI | ||||||
Components | Ribonuclease HI | ||||||
Keywords | HYDROLASE / stability / cavity / Endonuclease / Magnesium / Metal-binding / Nuclease | ||||||
Function / homology | Function and homology information DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / endonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Takano, K. | ||||||
Citation | Journal: Protein Pept.Lett. / Year: 2010 Title: Protein core adaptability: crystal structures of the cavity-filling variants of Escherichia coli RNase HI Authors: Tanaka, M. / Chon, H. / Angkawidjaja, C. / 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 | 3aa5.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aa5.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 3aa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/3aa5 ftp://data.pdbj.org/pub/pdb/validation_reports/aa/3aa5 | HTTPS FTP |
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-Related 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: 17699.096 Da / Num. of mol.: 1 / Mutation: A52F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Y4, 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: 1.87 Å3/Da / Density % sol: 34.1 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→42.79 Å / Num. obs: 8637 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.79 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.833 / SU B: 5.749 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.255 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: 10.461 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→42.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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