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Open data
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Basic information
Entry | Database: PDB / ID: 1dix | ||||||
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Title | CRYSTAL STRUCTURE OF RNASE LE | ||||||
![]() | EXTRACELLULAR RIBONUCLEASE LE | ||||||
![]() | HYDROLASE / ALPHA PLUS BETA | ||||||
Function / homology | ![]() ribonuclease T2 / ribonuclease T2 activity / cell wall / RNA catabolic process / RNA endonuclease activity / lyase activity / RNA binding / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tanaka, N. / Nakamura, K.T. | ||||||
![]() | ![]() Title: Crystal structure of a plant ribonuclease, RNase LE. Authors: Tanaka, N. / Arai, J. / Inokuchi, N. / Koyama, T. / Ohgi, K. / Irie, M. / Nakamura, K.T. #1: ![]() Title: Crystallization and Preliminary X-ray Crystallographic Studies of Ribonuclease LE from Lycopersicon esculentum Authors: Tanaka, N. / Arai, J. / Inokuchi, N. / Koyama, T. / Ohgi, K. / Irie, M. / Nakamura, K.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.8 KB | Display | ![]() |
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PDB format | ![]() | 39.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370.9 KB | Display | ![]() |
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Full document | ![]() | 378.2 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 9.9 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 22912.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.27 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG1540, CITRATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 41 % | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 31, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→100 Å / Num. all: 144121 / Num. obs: 22385 / % possible obs: 93.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.049 |
Reflection | *PLUS Num. measured all: 144121 / Rmerge(I) obs: 0.054 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.65→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||
Refinement | *PLUS σ(F): 1 / Num. reflection Rfree: 2296 / % reflection Rfree: 10 % / Rfactor obs: 0.219 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |