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- PDB-3htg: 2-ethoxy-3,4-dihydro-2h-pyran in complex with T4 lysozyme L99A/M102Q -
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Open data
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Basic information
Entry | Database: PDB / ID: 3htg | ||||||
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Title | 2-ethoxy-3,4-dihydro-2h-pyran in complex with T4 lysozyme L99A/M102Q | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME / Antimicrobial | ||||||
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 | ![]() ![]() | ||||||
![]() | Boyce, S.E. / Mobley, D.L. / Rocklin, G.J. / Graves, A.P. / Dill, K.A. / Shoichet, B.K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94 KB | Display | ![]() |
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PDB format | ![]() | 70.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.1 KB | Display | ![]() |
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Full document | ![]() | 457.9 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ht6C ![]() 3ht7C ![]() 3ht8C ![]() 3ht9C ![]() 3htbC ![]() 3htdC ![]() 3htfC ![]() 3hu8C ![]() 3hu9C ![]() 3huaC ![]() 3hukC ![]() 3huqC ![]() 1lguS 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
#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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-BME / |
#4: Chemical | ChemComp-JZ7 / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % |
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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: ![]() ![]() ![]() |
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: 1.25→30 Å / Num. all: 53814 / Num. obs: 53814 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.29 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.46 |
Reflection shell | Resolution: 1.25→1.33 Å / Redundancy: 4.93 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4.8 / % possible all: 76.7 |
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Processing
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Refinement | Method to determine structure: REFMAC Starting model: PDB ENTRY 1LGU Resolution: 1.26→27.35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.314 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.041 / 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: 12.662 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→27.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.26→1.289 Å / Total num. of bins used: 20
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