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Yorodumi- PDB-6lck: TtGalA, alpha-galactosidase from Thermus thermophilus in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lck | |||||||||
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Title | TtGalA, alpha-galactosidase from Thermus thermophilus in complex with p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG) | |||||||||
Components | Alpha-galactosidase | |||||||||
Keywords | HYDROLASE / alpha-galactosidase / hexamer assembly / substrate specificity / thermostable / stachyose | |||||||||
Function / homology | Glycoside hydrolase family 36 / Melibiase / alpha-galactosidase activity / carbohydrate catabolic process / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / 4-nitrophenyl alpha-D-galactopyranoside / Alpha-galactosidase Function and homology information | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Chen, S.C. / Hsu, C.H. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: J.Agric.Food Chem. / Year: 2020 Title: Crystal Structure of alpha-Galactosidase fromThermus thermophilus: Insight into Hexamer Assembly and Substrate Specificity. Authors: Chen, S.C. / Wu, S.P. / Chang, Y.Y. / Hwang, T.S. / Lee, T.H. / Hsu, C.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lck.cif.gz | 355.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lck.ent.gz | 232.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lck_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6lck_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6lck_validation.xml.gz | 49.8 KB | Display | |
Data in CIF | 6lck_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/6lck ftp://data.pdbj.org/pub/pdb/validation_reports/lc/6lck | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53986.309 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Gene: TTHB115 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53W51 #2: Sugar | Has ligand of interest | Y | |
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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: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.1M CAPSO pH 9.2, 0.2M Li2SO4, 10% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→30 Å / Num. obs: 46936 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 47.39 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.85→2.95 Å / Rmerge(I) obs: 0.505 / Num. unique obs: 4617 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apo structure Resolution: 2.85→28.06 Å / SU ML: 0.3067 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4079
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→28.06 Å
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Refine LS restraints |
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LS refinement shell |
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