+Open data
-Basic information
Entry | Database: PDB / ID: 3huk | ||||||
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Title | Benzylacetate in complex with T4 lysozyme L99A/M102Q | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME / Antimicrobial | ||||||
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 / REFMAC / Resolution: 1.29 Å | ||||||
Authors | Boyce, S.E. / Mobley, D.L. / Rocklin, G.J. / Graves, A.P. / Dill, K.A. / Shoichet, B.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. Authors: Boyce, S.E. / Mobley, D.L. / Rocklin, G.J. / Graves, A.P. / Dill, K.A. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3huk.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3huk.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3huk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3huk_validation.pdf.gz | 458.6 KB | Display | wwPDB validaton report |
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Full document | 3huk_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 3huk_validation.xml.gz | 12 KB | Display | |
Data in CIF | 3huk_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/3huk ftp://data.pdbj.org/pub/pdb/validation_reports/hu/3huk | HTTPS FTP |
-Related structure data
Related structure data | 3ht6C 3ht7C 3ht8C 3ht9C 3htbC 3htdC 3htfC 3htgC 3hu8C 3hu9C 3huaC 3huqC 1lguS 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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 18646.316 Da / Num. of mol.: 1 / Mutation: S38D,L99A,M102Q,N144D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Strain: Enterobacteria Phage T4 Sensu Lato / Gene: E / Plasmid: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | ChemComp-J0Z / | ||
#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: 2.69 Å3/Da / Density % sol: 54.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11589 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11589 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→50 Å / Num. all: 51404 / Num. obs: 51404 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.055 / Χ2: 2.007 / Net I/σ(I): 54.919 |
Reflection shell | Resolution: 1.29→1.34 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.38 / Num. unique all: 5080 / Χ2: 1.056 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: REFMAC Starting model: PDB ENTRY 1LGU Resolution: 1.29→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.177 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.045 / 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 max: 78.52 Å2 / Biso mean: 14.402 Å2 / Biso min: 7.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.29→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.29→1.323 Å / Total num. of bins used: 20
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