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- PDB-4po3: Crystal structure of a C4-C4 SN3 tributyrin phosphonate inhibited... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4po3 | ||||||
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Title | Crystal structure of a C4-C4 SN3 tributyrin phosphonate inhibited by ESTERASE B from LACTOBACILLUS RHAMNOSIS | ||||||
![]() | Esterase B | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bennett, M.D. / Anderson, B.F. / Norris, G.E. / Colbert, D.A. | ||||||
![]() | ![]() Title: Crystal structure of a C4-C4 SN3 tributyrin phodphonate inhibited ESTERASE B from LACTOBACILLUS RHAMNOSIS Authors: Bennett, M.D. / Colbert, D.A. / Anderson, B.F. / Norris, G.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.6 KB | Display | ![]() |
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PDB format | ![]() | 58.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4n5hS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 35794.027 Da / Num. of mol.: 1 / Mutation: V218A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HY4 / ( |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.81 % |
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Crystal grow![]() | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0 ammonium phosphate, 0.1M TrisHCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 20, 2006 |
Radiation | Monochromator: Capillary Focusing Optics and Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.44→38.84 Å / Num. obs: 24173 / % possible obs: 89.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.73 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.44→1.49 Å / Redundancy: 1.26 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.4 / % possible all: 25.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 4N5H Resolution: 1.96→38.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.67 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.138 / 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: 25.301 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→38.84 Å
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Refine LS restraints |
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