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Yorodumi- PDB-2rn2: STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rn2 | ||||||
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Title | STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION | ||||||
Components | RIBONUCLEASE H | ||||||
Keywords | HYDROLASE(ENDORIBONUCLEASE) | ||||||
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 / Resolution: 1.48 Å | ||||||
Authors | Katayanagi, K. / Miyagawa, M. / Matsushima, M. / Ishikawa, M. / Kanaya, S. / Nakamura, H. / Ikehara, M. / Matsuzaki, T. / Morikawa, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1992 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. #1: Journal: Nature / Year: 1990 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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Remark 700 | SHEET THE FOLLOWING IS THE CORRESPONDENCE BETWEEN THE SHEET RECORDS IN THIS ENTRY AND THE BETA- ...SHEET THE FOLLOWING IS THE CORRESPONDENCE BETWEEN THE SHEET RECORDS IN THIS ENTRY AND THE BETA-STRANDS DEFINED IN THE PAPER ENTITLED THREE-DIMENSIONAL STRUCTURE OF RIBONUCLEASE H FROM E. COLI (K.KATAYANAGI ET AL. NATURE (1990) VOL.347 PP 306-309). STRAND 1 (RIGHT ARROW) BETA C STRAND 2 (RIGHT ARROW) BETA B STRAND 3 (RIGHT ARROW) BETA A STRAND 4 (RIGHT ARROW) BETA D STRAND 5 (RIGHT ARROW) BETA E |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rn2.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rn2.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 2rn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rn2_validation.pdf.gz | 364 KB | Display | wwPDB validaton report |
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Full document | 2rn2_full_validation.pdf.gz | 369.7 KB | Display | |
Data in XML | 2rn2_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 2rn2_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/2rn2 ftp://data.pdbj.org/pub/pdb/validation_reports/rn/2rn2 | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Atom site foot note | 1: RESIDUE 17 IS A CIS PROLINE. |
-Components
#1: Protein | Mass: 17622.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) 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 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.1 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 9 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.48 Å / Lowest resolution: 9999 Å / Num. all: 23454 / % possible obs: 73.4 % / Num. measured all: 17254 / Rmerge(I) obs: 0.0576 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.196 / Highest resolution: 1.48 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.48 Å
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Refine LS restraints |
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Software | *PLUS Name: 'PROLSQ' / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.48 Å / Lowest resolution: 6 Å / Num. reflection obs: 16851 / σ(I): 1 / Rfactor obs: 0.196 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.48 Å / Lowest resolution: 6 Å / Total num. of bins used: 7 / Num. reflection obs: 2400 / Rfactor obs: 0.379 |