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- PDB-3hh4: New azaborine compounds bind to the T4 lysozyme L99A cavity - Ben... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hh4 | ||||||
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Title | New azaborine compounds bind to the T4 lysozyme L99A cavity - Benzene as control | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / azaborine / T4 lysozyme / ligand binding / hydrophobic cavity / 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: Boron mimetics: 1,2-dihydro-1,2-azaborines bind inside a nonpolar cavity of T4 lysozyme. Authors: Liu, L. / Marwitz, A.J. / Matthews, B.W. / Liu, S.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.2 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hh3C ![]() 3hh5C ![]() 3hh6C ![]() 3dmvS C: citing same article ( S: Starting model for refinement |
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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
#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.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-BNZ / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 2.0-2.2M K/Na phosphase, 50mM BME, 50mM HED (vapor-diffusion for complex preparation), pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2009 / Details: Si(220) |
Radiation | Monochromator: 0.9791 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→51.96 Å / Num. obs: 57244 / % possible obs: 100 % / Observed criterion σ(I): 5 / Redundancy: 15.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 34.3 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 10.7 / Num. unique all: 2834 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DMV Resolution: 1.25→51.96 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.018 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 15.664 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→51.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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