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- PDB-6gvd: Alpha-galactosidase from Thermotoga maritima in complex with cycl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gvd | ||||||
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Title | Alpha-galactosidase from Thermotoga maritima in complex with cyclohexene-based carbasugar mimic of galactose | ||||||
![]() | Alpha-galactosidase | ||||||
![]() | HYDROLASE / glycoside hydrolase / galactosidase / carbohydrate processing enzyme / inhibitor | ||||||
Function / homology | ![]() alpha-galactosidase / alpha-galactosidase activity / glycoside catabolic process / carbohydrate binding / carbohydrate metabolic process / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gloster, T.M. / Pengelly, R.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level. Authors: Ren, W. / Pengelly, R. / Farren-Dai, M. / Shamsi Kazem Abadi, S. / Oehler, V. / Akintola, O. / Draper, J. / Meanwell, M. / Chakladar, S. / Swiderek, K. / Moliner, V. / Britton, R. / Gloster, T.M. / Bennet, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276 KB | Display | ![]() |
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PDB format | ![]() | 218.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 782.2 KB | Display | ![]() |
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Full document | ![]() | 786 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 47.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gtaC ![]() 6gwfC ![]() 6gwgC ![]() 6gx8C ![]() 5m0xS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 66198.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Electron density at the N- and C-terminus was disordered and could not be modelled in the structure. Source: (gene. exp.) ![]() ![]() Gene: galA, TM_1192, Tmari_1199 Production host: ![]() ![]() References: UniProt: G4FEF4, alpha-galactosidase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FDK / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M MgSO4, 20% (w/v) poly(ethylene glycol) (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→68.59 Å / Num. obs: 185329 / % possible obs: 98.8 % / Redundancy: 5.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.029 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.22→1.25 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 12780 / CC1/2: 0.497 / Rpim(I) all: 0.506 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5M0X Resolution: 1.22→68.59 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.893 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.041 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.862 Å2
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Refinement step | Cycle: 1 / Resolution: 1.22→68.59 Å
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Refine LS restraints |
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