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Yorodumi- PDB-2yv0: Structural and Thermodynamic Analyses of E. coli ribonuclease HI ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yv0 | ||||||
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Title | Structural and Thermodynamic Analyses of E. coli ribonuclease HI Variant with Quintuple Thermostabilizing Mutations | ||||||
Components | Ribonuclease HI | ||||||
Keywords | HYDROLASE / RNase HI / Quintuple Thermostabilizing Mutations / E. coli | ||||||
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: 1.4 Å | ||||||
Authors | Haruki, M. / Motegi, T. / Tadokoro, T. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
Citation | Journal: Febs J. / Year: 2007 Title: Structural and thermodynamic analyses of Escherichia coli RNase HI variant with quintuple thermostabilizing mutations. Authors: Haruki, M. / Tanaka, M. / Motegi, T. / Tadokoro, T. / 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 | 2yv0.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yv0.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yv0 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yv0 | HTTPS FTP |
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-Related structure data
Related structure data | 2rn2S 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: 17560.949 Da / Num. of mol.: 1 / Mutation: G23A, H62P, V74L, K95G, D134H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rnhA / Plasmid: pJLA503 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P0A7Y4, ribonuclease H |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.82 % |
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Crystal grow | Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 Å |
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Detector | Date: Mar 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→50 Å / Num. obs: 31520 / % possible obs: 99.8 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 62 |
Reflection shell | Resolution: 1.32→1.37 Å / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 12.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RN2 Resolution: 1.4→25.91 Å / Cor.coef. Fo:Fc: 0.956 / SU B: 1.183 / SU ML: 0.049 / ESU R: 0.068 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.709 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→25.91 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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