+Open data
-Basic information
Entry | Database: PDB / ID: 2mll | ||||||
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Title | MISTLETOE LECTIN I FROM VISCUM ALBUM | ||||||
Components | (PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)) x 2 | ||||||
Keywords | RIBOSOME / RIBOSOME-INACTIVATING PROTEIN TYPE II | ||||||
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: 2.7 Å | ||||||
Authors | Krauspenhaar, R. / Eschenburg, S. / Perbandt, M. / Kornilov, V. / Konareva, N. / Mikailova, I. / Stoeva, S. / Wacker, R. / Maier, T. / Singh, T.P. ...Krauspenhaar, R. / Eschenburg, S. / Perbandt, M. / Kornilov, V. / Konareva, N. / Mikailova, I. / Stoeva, S. / Wacker, R. / Maier, T. / Singh, T.P. / Mikhailov, A. / Voelter, W. / Betzel, C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 1999 Title: Crystal structure of mistletoe lectin I from Viscum album. Authors: Krauspenhaar, R. / Eschenburg, S. / Perbandt, M. / Kornilov, V. / Konareva, N. / Mikailova, I. / Stoeva, S. / Wacker, R. / Maier, T. / Singh, T. / Mikhailov, A. / Voelter, W. / Betzel, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mll.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mll.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 2mll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mll_validation.pdf.gz | 407.1 KB | Display | wwPDB validaton report |
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Full document | 2mll_full_validation.pdf.gz | 478.3 KB | Display | |
Data in XML | 2mll_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 2mll_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/2mll ftp://data.pdbj.org/pub/pdb/validation_reports/ml/2mll | HTTPS FTP |
-Related structure data
Related structure data | 1ce7C 2aaiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25656.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: Q6ITZ3*PLUS | ||
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#2: Protein | Mass: 27072.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viscum album (European mistletoe) / References: UniProt: P81830, UniProt: Q6ITZ3*PLUS | ||
#3: Sugar | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 4.94 Å3/Da / Density % sol: 75.08 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4 | |||||||||||||||||||||||||||||||||||
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: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.06 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→10 Å / Num. obs: 29232 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.025 |
Reflection shell | Resolution: 2.7→10 Å / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 334925 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 97.9 % / Rmerge(I) obs: 0.181 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AAI Resolution: 2.7→8 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.248 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |