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- PDB-4jtp: Crystal structure of Ribosome inactivating protein from Momordica... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jtp | ||||||
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Title | Crystal structure of Ribosome inactivating protein from Momordica balsamina complexed with Ascorbic acid at 1.85 Angstrom resolution | ||||||
![]() | rRNA N-glycosidase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pandey, S. / Bhushan, A. / Singh, A. / Tyagi, T.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
![]() | ![]() Title: Crystal structure of Ribosome inactivating protein from Momordica balsamina complexed with Ascorbic acid at 1.85 Angstrom resolution Authors: Pandey, S. / Bhushan, A. / Singh, A. / Tyagi, T.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.3 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 316.4 KB | Display | ![]() |
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Full document | ![]() | 317 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g2x S: Starting model for refinement |
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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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Components
#1: Protein | ![]() Mass: 27093.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-NAG / ![]() |
#3: Sugar | ChemComp-ASC / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.27 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 17, 2012 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→37.67 Å / Num. all: 20151 / Num. obs: 20151 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.052 / Net I/σ(I): 44.3 |
Reflection shell | Resolution: 1.85→1.88 Å / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4G2X ![]() 4g2x Resolution: 1.85→37.6 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.138 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.421 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→37.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.849→1.897 Å / Total num. of bins used: 20
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