+Open data
-Basic information
Entry | Database: PDB / ID: 2v9b | ||||||
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Title | X-ray structure of viscotoxin B2 from Viscum album | ||||||
Components | VISCOTOXIN-B | ||||||
Keywords | TOXIN / THIONIN / SECRETED / PLANT TOXIN / PLANT DEFENSE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | VISCUM ALBUM (European mistletoe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.05 Å | ||||||
Authors | Debreczeni, J.E. / Pal, A. / Kahle, B. / Zeeck, A. / Sheldrick, G.M. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2008 Title: Structures of viscotoxins A1 and B2 from European mistletoe solved using native data alone. Authors: Pal, A. / Debreczeni, J.E. / Sevvana, M. / Gruene, T. / Kahle, B. / Zeeck, A. / Sheldrick, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v9b.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v9b.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 2v9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v9b_validation.pdf.gz | 413.4 KB | Display | wwPDB validaton report |
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Full document | 2v9b_full_validation.pdf.gz | 413.8 KB | Display | |
Data in XML | 2v9b_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 2v9b_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/2v9b ftp://data.pdbj.org/pub/pdb/validation_reports/v9/2v9b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (9.0E-6, 0.9913, -0.1315), Vector: |
-Components
#1: Protein/peptide | Mass: 4865.536 Da / Num. of mol.: 2 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) VISCUM ALBUM (European mistletoe) / References: UniProt: P08943 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | N11D KNOWN ISOFORM MUTATION | |
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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: 1.7 Å3/Da / Density % sol: 30 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1UL HANGING DROP, 30 MG/ML PROTEIN, 0.2M AMSO4, 0.08M CACODYLATE PH 6.5, 25% PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→20 Å / Num. obs: 34317 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 21.34 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.05→1.15 Å / Redundancy: 21 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 12.6 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS Starting model: NONE Resolution: 1.05→40 Å / Num. parameters: 7604 / Num. restraintsaints: 10158 / Cross valid method: THROUGHOUT / σ(F): 12 / Stereochemistry target values: ENGH AND HUBER / Details: HYDROGEN ATOMS WERE ADDED IN RIDING POSITIONS
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Refine analyze | Num. disordered residues: 14 / Occupancy sum hydrogen: 646 / Occupancy sum non hydrogen: 795 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→40 Å
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Refine LS restraints |
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