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Yorodumi- PDB-8skm: Wild type chlorogenic acid esterase from Lactobacillus helveticus -
+Open data
-Basic information
Entry | Database: PDB / ID: 8skm | |||||||||
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Title | Wild type chlorogenic acid esterase from Lactobacillus helveticus | |||||||||
Components | Chlorogenic acid esterase | |||||||||
Keywords | HYDROLASE / Chlorogenic acid / esterase / ferulic acid esterase / insertion domain | |||||||||
Function / homology | Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / aminopeptidase activity / Alpha/Beta hydrolase fold / Alpha/beta hydrolase Function and homology information | |||||||||
Biological species | Lactobacillus helveticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Owens, C.P. / Okumura, T.L.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Febs Lett. / Year: 2023 Title: The structure of a Lactobacillus helveticus chlorogenic acid esterase and the dynamics of its insertion domain provide insights into substrate binding. Authors: Omori, K.K. / Drucker, C.T. / Okumura, T.L.S. / Carl, N.B. / Dinn, B.T. / Ly, D. / Sacapano, K.N. / Tajii, A. / Owens, C.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8skm.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8skm.ent.gz | 128.9 KB | Display | PDB format |
PDBx/mmJSON format | 8skm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/8skm ftp://data.pdbj.org/pub/pdb/validation_reports/sk/8skm | HTTPS FTP |
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-Related structure data
Related structure data | 8sljC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27880.467 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus helveticus (bacteria) / Gene: BCM45_08315 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0D5MKR6 #2: 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: 4.21 Å3/Da / Density % sol: 70.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: citric acid, PEG 6000, lithium chloride |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→37.92 Å / Num. obs: 649288 / % possible obs: 99.04 % / Redundancy: 9.3 % / Biso Wilson estimate: 26.68 Å2 / CC1/2: 0.926 / Rmerge(I) obs: 0.5713 / Rpim(I) all: 0.196 / Net I/σ(I): 7.54 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.645 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6651 / CC1/2: 0.339 / CC star: 0.712 / Rpim(I) all: 0.559 / % possible all: 94.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→35.91 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.98 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→35.91 Å
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Refine LS restraints |
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LS refinement shell |
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