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Open data
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Basic information
Entry | Database: PDB / ID: 1kvc | ||||||
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Title | E. COLI RIBONUCLEASE HI D134N MUTANT | ||||||
![]() | RIBONUCLEASE H![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Kashiwagi, T. / Jeanteur, D. / Haruki, M. / Katayanagi, K. / Kanaya, S. / Morikawa, K. | ||||||
![]() | ![]() Title: Proposal for new catalytic roles for two invariant residues in Escherichia coli ribonuclease HI. Authors: Kashiwagi, T. / Jeanteur, D. / Haruki, M. / Katayanagi, K. / Kanaya, S. / Morikawa, K. #1: ![]() Title: Crystal Structure of Escherichia Coli Rnase Hi in Complex with Mg2+ at 2.8 A Resolution: Proof for a Single Mg(2+)-Binding Site Authors: Katayanagi, K. / Okumura, M. / Morikawa, K. #2: ![]() Title: Structural Details of Ribonuclease H from Escherichia Coli as Refined to an Atomic Resolution Authors: Katayanagi, K. / Miyagawa, M. / Matsushima, M. / Ishikawa, M. / Kanaya, S. / Nakamura, H. / Ikehara, M. / Matsuzaki, T. / Morikawa, K. #3: ![]() Title: Structure of Ribonuclease H Phased at 2 A Resolution by MAD Analysis of the Selenomethionyl Protein Authors: Yang, W. / Hendrickson, W.A. / Crouch, R.J. / Satow, Y. #4: ![]() Title: Three-Dimensional Structure of Ribonuclease H from E. Coli Authors: Katayanagi, K. / Miyagawa, M. / Matsushima, M. / Ishikawa, M. / Kanaya, S. / Ikehara, M. / Matsuzaki, T. / Morikawa, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.9 KB | Display | ![]() |
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PDB format | ![]() | 32.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 17622.012 Da / Num. of mol.: 1 / Mutation: D134N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.7 % | ||||||||||||||||||||
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Crystal grow![]() | *PLUS Temperature: 20 ℃ / pH: 9 / Method: vapor diffusion, hanging drop / Details: macro-seeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 8, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Highest resolution: 1.9 Å / Num. obs: 9319 / % possible obs: 83.8 % / Observed criterion σ(I): 0.5 / Redundancy: 5.07 % / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.93 Å / % possible obs: 62.7 % |
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Processing
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Refinement | Resolution: 1.9→6 Å / σ(F): 1 Details: IDEAL BOND LENGTHS AND ANGLES USED DURING REFINEMENT: HENDRICKSON AND KONNERT INITIAL REFINEMENTS WERE DONE WITH X-PLOR 3.1 BY BRUNGER.
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Displacement parameters | Biso mean: 23.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |