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Open data
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Basic information
Entry | Database: PDB / ID: 1hwp | |||||||||
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Title | EBULIN COMPLEXED WITH PTEROIC ACID, TRIGONAL CRYSTAL FORM | |||||||||
![]() | (EBULIN) x 2 | |||||||||
![]() | HYDROLASE / Ribosome-inactivating protein / ricin-like / inhibitor | |||||||||
Function / homology | ![]() rRNA N-glycosylase / rRNA N-glycosylase activity / metabolic process / defense response / toxin activity / negative regulation of translation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Pascal, J.M. / Day, P.J. / Monzingo, A.F. / Ernst, S.R. / Robertus, J.D. | |||||||||
![]() | ![]() Title: 2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l. Authors: Pascal, J.M. / Day, P.J. / Monzingo, A.F. / Ernst, S.R. / Robertus, J.D. / Iglesias, R. / Perez, Y. / Ferreras, J.M. / Citores, L. / Girbes, 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 | ![]() | 108.3 KB | Display | ![]() |
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PDB format | ![]() | 82.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hwmC ![]() 1hwnC ![]() 1hwoSC C: citing same article ( 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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1 |
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 28478.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: N-GLYCOSIDASE / Source: (natural) ![]() |
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#2: Protein | Mass: 29377.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GALACTOSIDE SPECIFIC LECTIN / Source: (natural) ![]() |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
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#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 21 molecules ![](data/chem/img/PT1.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-PT1 / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.13 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.1 M Na,K Tartrate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 21, 1998 |
Radiation | Monochromator: Double focusing mirrors, (Ni + Pt) + Ni filters Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. all: 11311 / Num. obs: 11311 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.378 / % possible all: 98.1 |
Reflection shell | *PLUS % possible obs: 98.1 % / Mean I/σ(I) obs: 2.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HWO Resolution: 3.1→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.1→40 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refine LS restraints | *PLUS
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