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Yorodumi- PDB-1rdd: CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE HI IN COMPLEX WITH MG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rdd | ||||||
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Title | CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE HI IN COMPLEX WITH MG2+ AT 2.8 ANGSTROMS RESOLUTION: PROOF FOR A SINGLE MG2+ SITE | ||||||
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: 2.8 Å | ||||||
Authors | Katayanagi, K. / Morikawa, K. | ||||||
Citation | Journal: Proteins / Year: 1993 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. #1: 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. #2: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rdd.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rdd.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rdd_validation.pdf.gz | 411.9 KB | Display | wwPDB validaton report |
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Full document | 1rdd_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 1rdd_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1rdd_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/1rdd ftp://data.pdbj.org/pub/pdb/validation_reports/rd/1rdd | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.12 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 8.9 / PH range high: 8.2 | ||||||||||||||||||||||||||||||||||||
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: 3953 / % possible obs: 90.1 % / Num. measured all: 15785 / Rmerge(I) obs: 0.095 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.19 / Highest resolution: 2.8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.8 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 / Rfactor obs: 0.19 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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