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Yorodumi- PDB-3dn3: Iodopentafluorobenzene binding in the hydrophobic cavity of T4 ly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dn3 | ||||||
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Title | Iodopentafluorobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / T4 lysozyme / halogen bond / hydrophobic cavity / halogenated benzene / Antimicrobial / Bacteriolytic enzyme / Glycosidase | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Bacteriophage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Liu, L. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding. Authors: Liu, L. / Baase, W.A. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dn3.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dn3.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 3dn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dn3_validation.pdf.gz | 815.1 KB | Display | wwPDB validaton report |
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Full document | 3dn3_full_validation.pdf.gz | 815.6 KB | Display | |
Data in XML | 3dn3_validation.xml.gz | 11 KB | Display | |
Data in CIF | 3dn3_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/3dn3 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/3dn3 | HTTPS FTP |
-Related structure data
Related structure data | 3dmvSC 3dmxC 3dmzC 3dn0C 3dn1C 3dn2C 3dn4C 3dn6C 3dn8C 3dnaC 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: 18586.283 Da / Num. of mol.: 1 / Mutation: C54T, C97A, L99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteriophage T4 (virus) / Gene: E / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-IBF / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 2.0-2.2 M K/Na phosphate, pH 6.9, 5mM BME and 5mM oxidized BME. Complexes were prepared by soaking or vapor diffusion methods, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2005 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→53 Å / Num. obs: 17811 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3DMV Resolution: 1.8→27.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.226 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.521 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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