+
Open data
-
Basic information
Entry | Database: PDB / ID: 1oql | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Mistletoe Lectin I from Viscum album complexed with galactose | |||||||||
![]() | (MISTLETOE LECTIN ...) x 2 | |||||||||
![]() | HYDROLASE/SUGAR BINDING PROTEIN / Type-II ribosome-inactivating protein / ricin-like / beta-trefoil / HYDROLASE-SUGAR BINDING PROTEIN COMPLEX | |||||||||
Function / homology | ![]() rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Niwa, H. / Tonevitsky, A.G. / Agapov, I.I. / Saward, S. / Pfuller, U. / Palmer, R.A. | |||||||||
![]() | ![]() Title: Crystal structure at 3 A of mistletoe lectin I, a dimeric type-II ribosome-inactivating protein, complexed with galactose Authors: Niwa, H. / Tonevitsky, A.G. / Agapov, I.I. / Saward, S. / Pfuller, U. / Palmer, R.A. #1: ![]() Title: Mistletoe lectin I forms a double trefoil structure Authors: Sweeney, E.C. / Tonevitsky, A.G. / Palmer, R.A. / Niwa, H. / Pfuller, U. / Eck, J. / Lentzen, H. / Agapov, I.I. / Kirpichnikov, M.P. #2: ![]() Title: Crystallization of the ribosome inactivating protein ML1 from Viscum album (mistletoe) complexed with beta-D-galactose Authors: Sweeney, E.C. / Palmer, R.A. / Pfuller, U. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 115.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 88.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2aaiS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 |
| ||||||||
Unit cell |
|
-
Components
-MISTLETOE LECTIN ... , 2 types, 2 molecules AB
#1: Protein | Mass: 27866.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: GenBank: 3714429, UniProt: P81446*PLUS, rRNA N-glycosylase |
---|---|
#2: Protein | Mass: 28834.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/GAL.gif)
![](data/chem/img/GAL.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Sugar | |
---|
-Non-polymers , 1 types, 47 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.51 Å3/Da / Density % sol: 72.52 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.4 Details: 0.9M Ammonium sulphate, Glycine buffer, pH 3.4, 0.1M galactose, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40.2 Å / Num. all: 24175 / Num. obs: 24175 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 68126 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Ricin (PDB 2AAI) Resolution: 3→40.2 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2326178.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: OXT was included for the A-chain in the refinement, but removed on deposition.
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.314132 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→40.2 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|