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- PDB-3dna: Iodobenzene binding in the hydrophobic cavity of T4 lysozyme L99A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dna | ||||||
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Title | Iodobenzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant (seleno version) | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / T4 lysozyme / halogen bond / hydrophobic cavity / halogenated benzene / Antimicrobial / Bacteriolytic enzyme / Glycosidase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Liu, L. / Matthews, B.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.4 KB | Display | ![]() |
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PDB format | ![]() | 38.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455 KB | Display | ![]() |
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Full document | ![]() | 456.2 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dmvSC ![]() 3dmxC ![]() 3dmzC ![]() 3dn0C ![]() 3dn1C ![]() 3dn2C ![]() 3dn3C ![]() 3dn4C ![]() 3dn6C ![]() 3dn8C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18820.760 Da / Num. of mol.: 1 / Mutation: C54T, C97A, L99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 277 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HED.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/PIH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HED.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/PIH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PO4 / | ||||||
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#3: Chemical | ChemComp-CL / | ||||||
#4: Chemical | #5: Chemical | ChemComp-BME / | #6: Chemical | ChemComp-PIH / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % |
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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: ![]() |
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: 1.7→53 Å / Num. obs: 23070 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3DMV Resolution: 1.7→20.17 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.96 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / 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: 17.432 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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