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Yorodumi- PDB-1w2t: beta-fructosidase from Thermotoga maritima in complex with raffinose -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w2t | |||||||||
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Title | beta-fructosidase from Thermotoga maritima in complex with raffinose | |||||||||
Components | BETA FRUCTOSIDASE | |||||||||
Keywords | HYDROLASE / GLYCOSIDASE / INVERTASE / RAFFINOSE / BETA FRUCTOSIDASE | |||||||||
Function / homology | Function and homology information beta-fructofuranosidase activity / beta-fructofuranosidase / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | |||||||||
Authors | Alberto, F. / Henrissat, B. / Czjzek, M. | |||||||||
Citation | Journal: Biochem.J. / Year: 2006 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w2t.cif.gz | 554.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w2t.ent.gz | 458.1 KB | Display | PDB format |
PDBx/mmJSON format | 1w2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w2t_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 1w2t_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 1w2t_validation.xml.gz | 112 KB | Display | |
Data in CIF | 1w2t_validation.cif.gz | 162 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/1w2t ftp://data.pdbj.org/pub/pdb/validation_reports/w2/1w2t | HTTPS FTP |
-Related structure data
Related structure data | 1uypS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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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.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 Description: STRAIN MSB8 (DSM 3109) KINDLY PROVIDED BY DR. W. LIEBL Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O33833, beta-fructofuranosidase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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