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- PDB-1ril: CRYSTAL STRUCTURE OF RIBONUCLEASE H FROM THERMUS THERMOPHILUS HB8... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ril | ||||||
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Title | CRYSTAL STRUCTURE OF RIBONUCLEASE H FROM THERMUS THERMOPHILUS HB8 REFINED AT 2.8 ANGSTROMS RESOLUTION | ||||||
![]() | RIBONUCLEASE H | ||||||
![]() | HYDROLASE(ENDORIBONUCLEASE) | ||||||
Function / homology | ![]() DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Ishikawa, K. / Okumura, M. / Katayanagi, K. / Kimura, S. / Kanaya, S. / Nakamura, H. / Morikawa, K. | ||||||
![]() | ![]() Title: Crystal structure of ribonuclease H from Thermus thermophilus HB8 refined at 2.8 A resolution. Authors: Ishikawa, K. / Okumura, M. / Katayanagi, K. / Kimura, S. / Kanaya, S. / Nakamura, H. / Morikawa, K. #1: ![]() Title: Crystallization and Preliminary Crystallographic Analysis of Ribonuclease H from Thermus Thermophilus Hb8 Authors: Okumura, M. / Ishikawa, K. / Kanaya, S. / Itaya, M. / 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 | ![]() | 40.7 KB | Display | ![]() |
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PDB format | ![]() | 28.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 365.7 KB | Display | ![]() |
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Full document | ![]() | 382.1 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: RESIDUE 17 IS A CIS PROLINE. |
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Components
#1: Protein | Mass: 18763.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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Sequence details | THE NUMBERING OF THE AMINO ACIDS CONFORMS TO THAT OF ESCHERICHIA COLI RNASE HI, IN ORDER TO ...THE NUMBERING OF THE AMINO ACIDS CONFORMS TO THAT OF ESCHERICHI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.11 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 9.8 / Method: unknownDetails: taken from Okumura, M. et al (1993). Proteins Struct. Funct. Genet., 15, 108-111. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 4766 / % possible obs: 89 % / Observed criterion σ(I): 1 / Num. measured all: 46156 / Rmerge(I) obs: 0.093 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.8→8 Å / σ(F): 1 Details: THERE ARE TWO REGIONS OF LOW (OR NO) DENSITY, CONSISTING OF MET -4 - PRO 1 (N TERMINUS) AND PRO 148 - ALA 161 (C TERMINUS).
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 4766 / σ(F): 1 / Rfactor obs: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |