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- PDB-1rnb: CRYSTAL STRUCTURE OF A BARNASE-D(*GP*C) COMPLEX AT 1.9 ANGSTROMS ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rnb | ||||||
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Title | CRYSTAL STRUCTURE OF A BARNASE-D(*GP*C) COMPLEX AT 1.9 ANGSTROMS RESOLUTION | ||||||
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![]() | ENDONUCLEASE | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Janin, J. / Baudet, S. | ||||||
![]() | ![]() Title: Crystal structure of a barnase-d(GpC) complex at 1.9 A resolution. Authors: Baudet, S. / Janin, J. #1: ![]() Title: Molecular Structures of a New Family of Ribonucleases Authors: Mauguen, Y. / Hartley, R.W. / Dodson, E.J. / Dodson, G.G. / Bricogne, G. / Chothia, C. / Jack, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.9 KB | Display | ![]() |
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PDB format | ![]() | 25.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387.8 KB | Display | ![]() |
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Full document | ![]() | 400.3 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 8.2 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: THE SIDE CHAINS OF RESIDUES 2, 59, 60, AND 62 HAVE NO DENSITY. |
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Components
#1: DNA chain | Mass: 573.430 Da / Num. of mol.: 1 / Source method: obtained synthetically References: Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#2: Protein | Mass: 12398.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.36 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / 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: 1.9 Å / Num. obs: 12204 / Num. measured all: 26792 / Rmerge(I) obs: 0.058 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.214 / Highest resolution: 1.9 Å Details: THE DINUCLEOTIDE IS BOUND IN NON-PRODUCTIVE MODE AND IS INVOLVED IN CRYSTAL CONTACTS. THE SIDE CHAINS OF RESIDUES 2, 59, 60, AND 62 HAVE NO DENSITY. | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 5.5 Å / Num. reflection all: 10578 / Num. reflection obs: 9679 / σ(F): 3 / Rfactor obs: 0.214 / Rfactor Rwork: 0.214 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.6 Å2 | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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