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- PDB-1w2t: beta-fructosidase from Thermotoga maritima in complex with raffinose -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w2t | |||||||||
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Title | beta-fructosidase from Thermotoga maritima in complex with raffinose | |||||||||
![]() | BETA FRUCTOSIDASE | |||||||||
![]() | HYDROLASE / GLYCOSIDASE / INVERTASE / RAFFINOSE / BETA FRUCTOSIDASE | |||||||||
Function / homology | ![]() beta-fructofuranosidase activity / beta-fructofuranosidase / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Alberto, F. / Henrissat, B. / Czjzek, M. | |||||||||
![]() | ![]() Title: Crystal Structure of Inactivated Thermotoga Maritima Invertase in Complex with the Trisaccharide Substrate Raffinose. Authors: Alberto, F. / Jordi, E. / Henrissat, B. / Czjzek, M. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 554.3 KB | Display | ![]() |
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PDB format | ![]() | 458.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 112 KB | Display | |
Data in CIF | ![]() | 162 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uypS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 1 - 432 / Label seq-ID: 1 - 432
NCS oper:
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Components
#1: Protein | Mass: 49872.168 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: STRAIN MSB8 (DSM 3109) KINDLY PROVIDED BY DR. W. LIEBL Plasmid: PDEST17 / Production host: ![]() ![]() #2: Polysaccharide | beta-D-fructofuranose-(2-1)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CIT / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Compound details | CHAIN A-F ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: HANGING DROP TECHNIQUE 10% PEG 1000, 50 MM LI2SO4, 100 MM CITRATE PHOSPHATE BUFFER PH 4.2, CONCENTRATION PROTEIN 8 MG/ML, INCUBATION TEMPERATURE 20 C |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→129.099 Å / Num. obs: 225700 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.87→30 Å / Redundancy: 3 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 3.9 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UYP Resolution: 1.87→40 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.25 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.146 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→40 Å
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Refine LS restraints |
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