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Yorodumi- PDB-1lav: STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY CAVITY-FILLI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lav | ||||||
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Title | STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY CAVITY-FILLING MUTATIONS WITHIN A HYDROPHOBIC CORE | ||||||
Components | RIBONUCLEASE H | ||||||
Keywords | HYDROLASE | ||||||
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: 1.8 Å | ||||||
Authors | Ishikawa, K. / Nakamura, H. / Morikawa, K. / Kanaya, S. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core. Authors: Ishikawa, K. / Nakamura, H. / Morikawa, K. / Kanaya, S. #1: Journal: Protein Eng. / Year: 1993 Title: Structural Study of Mutants of Escherichia Coli Ribonuclease Hi with Enhanced Thermostability Authors: Ishikawa, K. / Kimura, S. / Kanaya, S. / Morikawa, K. / Nakamura, H. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Structural Details of Ribonuclease H from Escherichia Coli as Refined at an Atomic Resolution Authors: Katayanagi, K. / Miyagawa, M. / Matsushima, M. / Ishikawa, M. / Kanaya, S. / Nakamura, H. / Ikehara, M. / Matsuzaki, T. / Morikawa, K. #3: 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 STRANDS IN THE SHEET RECORD BELOW ARE DEFINED AS FOLLOWS IN THE PAPER (KATAYANAGI ET AL. ...SHEET THE STRANDS IN THE SHEET RECORD BELOW ARE DEFINED AS FOLLOWS IN THE PAPER (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 | 1lav.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lav.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/1lav ftp://data.pdbj.org/pub/pdb/validation_reports/la/1lav | 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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Atom site foot note | 1: CIS PROLINE - PRO 17 |
-Components
#1: Protein | Mass: 17637.025 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: 1.93 Å3/Da / Density % sol: 36.22 % | ||||||||||||||||||||
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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
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→6 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 10201 / σ(F): 1 / Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |