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Yorodumi- PDB-4po3: Crystal structure of a C4-C4 SN3 tributyrin phosphonate inhibited... -
+Open data
-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 | ||||||
Components | Esterase B | ||||||
Keywords | HYDROLASE / Esterase/Lipase / Triacylglycerase / Hydrolysis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus rhamnosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Bennett, M.D. / Anderson, B.F. / Norris, G.E. / Colbert, D.A. | ||||||
Citation | Journal: TO BE PUBLISHED 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4po3.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4po3.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 4po3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/4po3 ftp://data.pdbj.org/pub/pdb/validation_reports/po/4po3 | 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 |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Lactobacillus rhamnosus (bacteria) / Strain: HN001 / Gene: LRH_10360 / Plasmid: pGEX_6P3_EstB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B2CZF4 |
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#2: Chemical | ChemComp-HY4 / ( |
#3: 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: 2.5 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: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å |
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: 1.5418 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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