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- PDB-3pfc: Crystal structure of the Lactobacillus johnsonii cinnamoyl estera... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pfc | ||||||
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Title | Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with ferulic acid | ||||||
![]() | Cinnamoyl esterase | ||||||
![]() | HYDROLASE / alpha/beta hydrolase fold / esterase / cinnamoyl/feruloyl esterase / hydroxycinammates / extracellular | ||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stogios, P.J. / Lai, K.K. / Vu, C. / Xu, X. / Cui, H. / Molloy, S. / Gonzalez, C.F. / Yakunin, A. / Savchenko, A. | ||||||
![]() | ![]() Title: An Inserted alpha/beta Subdomain Shapes the Catalytic Pocket of Lactobacillus johnsonii Cinnamoyl Esterase Authors: Lai, K.K. / Stogios, P.J. / Vu, C. / Xu, X. / Cui, H. / Molloy, S. / Savchenko, A. / Yakunin, A. / Gonzalez, C.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.9 KB | Display | ![]() |
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PDB format | ![]() | 90 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 716.8 KB | Display | ![]() |
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Full document | ![]() | 719.9 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pf8C ![]() 3pf9C ![]() 3pfbC ![]() 3qm1C ![]() 3s2zC ![]() 3pfa 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30010.502 Da / Num. of mol.: 1 / Mutation: S106A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D3YEX6, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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-Non-polymers , 5 types, 230 molecules ![](data/chem/img/FER.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FER / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PE4 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 0.2 M lithium sulfate, 30% PEG4K, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 15, 2009 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. all: 25396 / Num. obs: 25396 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rsym value: 0.058 / Net I/σ(I): 22.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant Resolution: 1.75→17.649 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 16.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.613 Å2 / ksol: 0.397 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→17.649 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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