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Yorodumi- PDB-7y51: Acetylxylan esterase from Caldanaerobacter subterraneus subsp. te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y51 | ||||||||||||
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Title | Acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis TTE0866 delta100 mutant | ||||||||||||
Components | Predicted xylanase/chitin deacetylase | ||||||||||||
Keywords | HYDROLASE / Acetylxylan esterase | ||||||||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / hydrolase activity, acting on glycosyl bonds / xylan catabolic process Similarity search - Function | ||||||||||||
Biological species | Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||||||||
Authors | Sasamoto, K. / Himiyama, T. / Moriyoshi, K. / Ohmoto, T. / Uegaki, K. / Nakamura, T. / Nishiya, Y. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Febs Open Bio / Year: 2022 Title: Functional analysis of the N-terminal region of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis. Authors: Sasamoto, K. / Himiyama, T. / Moriyoshi, K. / Ohmoto, T. / Uegaki, K. / Nakamura, T. / Nishiya, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y51.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y51.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 7y51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/7y51 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/7y51 | HTTPS FTP |
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-Related structure data
Related structure data | 7fbwS S: Starting model for refinement |
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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: 22974.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: Cda1, TTE0866 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RBF4 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-NI / |
#4: 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: 4.3 Å3/Da / Density % sol: 71.41 % |
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Crystal grow | Temperature: 293 K / Method: evaporation, recrystallization / pH: 8 / Details: 20 mM Tris-HCl (pH8.0) 100 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→39.91 Å / Num. obs: 14957 / % possible obs: 99.9 % / Redundancy: 11 % / CC1/2: 0.993 / Rmerge(I) obs: 0.17 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.45→2.55 Å / Rmerge(I) obs: 0.912 / Num. unique obs: 1651 / CC1/2: 0.84 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7FBW Resolution: 2.45→39.91 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.681 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.188 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.227 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→39.91 Å
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Refine LS restraints |
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LS refinement shell |
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