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Yorodumi- PDB-3s2z: Crystal structure of the Lactobacillus johnsonii cinnamoyl estera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s2z | ||||||
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Title | Crystal structure of the Lactobacillus johnsonii cinnamoyl esterase LJ0536 S106A mutant in complex with caffeic acid | ||||||
Components | Cinnamoyl esterase | ||||||
Keywords | HYDROLASE / ALPHA/BETA HYDROLASE FOLD / ESTERASE / CINNAMOYL/FERULOYL ESTERASE / HYDROXYCINAMMATES | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / aminopeptidase activity Similarity search - Function | ||||||
Biological species | Lactobacillus johnsonii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Stogios, P.J. / Lai, K.K. / Vu, C. / Xu, X. / Cui, H. / Molloy, S. / Gonzalez, C.F. / Yakunin, A. / Savchenko, A. | ||||||
Citation | Journal: Plos One / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s2z.cif.gz | 228.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s2z.ent.gz | 181.7 KB | Display | PDB format |
PDBx/mmJSON format | 3s2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/3s2z ftp://data.pdbj.org/pub/pdb/validation_reports/s2/3s2z | HTTPS FTP |
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-Related structure data
Related structure data | 3pf8SC 3pf9C 3pfbC 3pfcC 3qm1C 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30010.502 Da / Num. of mol.: 2 / Mutation: S106A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus johnsonii (bacteria) / Gene: LJ0536 / Plasmid: P15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: D3YEX6, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Chemical | ChemComp-CL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M TRIS, 0.2 M LITHIUM SULPHATE, 30% PEG4K, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å | ||||||||||||||||||
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 15, 2010 | ||||||||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. all: 51281 / Num. obs: 51428 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.047 / Net I/σ(I): 21.86 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3PF8 Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.952 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.803 Å / Total num. of bins used: 20
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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