+Open data
-Basic information
Entry | Database: PDB / ID: 8yfz | ||||||
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Title | CRYSTAL STRUCTURE OF THE EST1 H274E MUTANT AT PH 4.2 | ||||||
Components | Carboxylesterase | ||||||
Keywords | HYDROLASE / ALPHA/BETA-HYDRORASE FOLD / CARBOXYLESTERASE | ||||||
Function / homology | Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine active site. / : / carboxylesterase / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / Carboxylesterase Function and homology information | ||||||
Biological species | Saccharolobus shibatae (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Unno, H. / Oshima, Y. / Nishino, T. / Nakayama, T. / Kusunoki, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biosci.Bioeng. / Year: 2024 Title: Lowering pH optimum of activity of SshEstI, a slightly alkaliphilic archaeal esterase of the hormone-sensitive lipase family. Authors: Ohara, K. / Oshima, Y. / Unno, H. / Nagano, S. / Kusunoki, M. / Takahashi, S. / Waki, T. / Yamashita, S. / Nakayama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yfz.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yfz.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 8yfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yfz_validation.pdf.gz | 655.5 KB | Display | wwPDB validaton report |
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Full document | 8yfz_full_validation.pdf.gz | 658.2 KB | Display | |
Data in XML | 8yfz_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 8yfz_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/8yfz ftp://data.pdbj.org/pub/pdb/validation_reports/yf/8yfz | HTTPS FTP |
-Related structure data
Related structure data | 8yfyC 1wzj 1wzp 1wzq 1wzr 1wzt 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33542.371 Da / Num. of mol.: 1 / Mutation: H274E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus shibatae (archaea) / Gene: SshEstI, J5U21_01394, J5U22_01308 / Plasmid: PTC99A / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NU42, carboxylesterase |
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#2: Sugar | ChemComp-BOG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 42.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.2 Details: 12% PEG 3000, 200MM NACL, 100MM PHOSPHATE-CITRATE, PH 4.2, VAPOR DIFFUSION, TEMPERATURE 293K PH range: 4.2 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Sep 22, 2003 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→18.6 Å / Num. obs: 46125 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 18.95 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 46125 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→18.34 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.114 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.069 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→18.34 Å
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Refine LS restraints |
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