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Yorodumi- PDB-3hh4: New azaborine compounds bind to the T4 lysozyme L99A cavity - Ben... -
+Open data
-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 | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / azaborine / T4 lysozyme / ligand binding / hydrophobic cavity / 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 | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Liu, L. / Matthews, B.W. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hh4.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hh4.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hh4_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 3hh4_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 3hh4_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 3hh4_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/3hh4 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/3hh4 | HTTPS FTP |
-Related structure data
Related structure data | 3hh3C 3hh5C 3hh6C 3dmvS C: citing same article (ref.) S: Starting model for refinement |
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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.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: p1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-BNZ / | #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: 2.67 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: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9791 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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