+Open data
-Basic information
Entry | Database: PDB / ID: 1oql | |||||||||
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Title | Mistletoe Lectin I from Viscum album complexed with galactose | |||||||||
Components | (MISTLETOE LECTIN ...) x 2 | |||||||||
Keywords | HYDROLASE/SUGAR BINDING PROTEIN / Type-II ribosome-inactivating protein / ricin-like / beta-trefoil / HYDROLASE-SUGAR BINDING PROTEIN COMPLEX | |||||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation Similarity search - Function | |||||||||
Biological species | Viscum album (European mistletoe) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Niwa, H. / Tonevitsky, A.G. / Agapov, I.I. / Saward, S. / Pfuller, U. / Palmer, R.A. | |||||||||
Citation | Journal: EUR.J.BIOCHEM. / Year: 2003 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: Journal: FEBS Lett. / Year: 1998 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: Journal: J.Mol.Biol. / Year: 1993 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oql.cif.gz | 115.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oql.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/1oql ftp://data.pdbj.org/pub/pdb/validation_reports/oq/1oql | HTTPS FTP |
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-Related structure data
Related structure data | 2aaiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-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) Viscum album (European mistletoe) References: GenBank: 3714429, UniProt: P81446*PLUS, rRNA N-glycosylase |
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#2: Protein | Mass: 28834.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: GenBank: 3714429, UniProt: P81446*PLUS |
-Sugars , 3 types, 6 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Sugar | |
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-Non-polymers , 1 types, 47 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.51 Å3/Da / Density % sol: 72.52 % | ||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.314132 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→40.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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