+Open data
-Basic information
Entry | Database: PDB / ID: 1okh | ||||||
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Title | Viscotoxin A3 from Viscum album L. | ||||||
Components | VISCOTOXIN A3 | ||||||
Keywords | TOXIN / THIONIN / PLANT DEFENSE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | VISCUM ALBUM (European mistletoe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Debreczeni, J.E. / Girmann, B. / Zeeck, A. / Sheldrick, G.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of Viscotoxin A3: Disulfide Location from Weak Sad Data Authors: Debreczeni, J.E. / Girmann, B. / Zeeck, A. / Kratzner, R. / 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 | 1okh.cif.gz | 26.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1okh.ent.gz | 20.3 KB | Display | PDB format |
PDBx/mmJSON format | 1okh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/1okh ftp://data.pdbj.org/pub/pdb/validation_reports/ok/1okh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.19986, -0.97837, -0.05339), Vector: |
-Components
#1: Protein/peptide | Mass: 4842.626 Da / Num. of mol.: 2 / Fragment: VISCOTOXIN A3 CHAIN, RESIDUES 27-72 / Source method: isolated from a natural source / Source: (natural) VISCUM ALBUM (European mistletoe) / Organ: LEAVES, STEMS / References: UniProt: P01538 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: 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: 1.79 Å3/Da / Density % sol: 31.5 % Description: DATA COLLECTED IN-HOUSE. PHASED USING IN-HOUSE SULFUR- SAD DATA | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 0.15M AM2SO4, 0.05M CACOD. PH=6.5, 30% PEG8000, 15MM HGCL2, pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / 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: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→68.59 Å / Num. obs: 8938 / % possible obs: 100 % / Redundancy: 5.25 % / Rmerge(I) obs: 0.0892 / Net I/σ(I): 14.31 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 4.42 % / Rmerge(I) obs: 0.3866 / Mean I/σ(I) obs: 3.89 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 1.75 Å / Redundancy: 5.3 % / Num. measured all: 50787 / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→20 Å / Num. parameters: 3115 / Num. restraintsaints: 2935 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 780 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.239 / Rfactor Rwork: 0.167 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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