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Yorodumi- PDB-1w18: Crystal Structure of levansucrase from Gluconacetobacter diazotro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w18 | ||||||
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Title | Crystal Structure of levansucrase from Gluconacetobacter diazotrophicus | ||||||
Components | LEVANSUCRASE | ||||||
Keywords | TRANSFERASE / FRUCTOSYL TRANSFERASE / GLYCOSYLTRANSFERASE | ||||||
Function / homology | Function and homology information levansucrase / levansucrase activity / carbohydrate utilization / extracellular region Similarity search - Function | ||||||
Biological species | GLUCONACETOBACTER DIAZOTROPHICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Martinez-Fleites, C. / Ortiz-Lombardia, M. / Pons, T. / Tarbouriech, N. / Taylor, E.J. / Hernandez, L. / Davies, G.J. | ||||||
Citation | Journal: Biochem.J. / Year: 2005 Title: Crystal Structure of Levansucrase from the Gram- Negative Bacterium Gluconacetobacter Diazotrophicus. Authors: Martinez-Fleites, C. / Ortiz-Lombardia, M. / Pons, T. / Tarbouriech, N. / Taylor, E.J. / Arrieta, J.G. / Hernandez, L. / Davies, G.J. | ||||||
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 | 1w18.cif.gz | 199.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w18.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 1w18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/1w18 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/1w18 | HTTPS FTP |
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-Related structure data
Related structure data | 1oygS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99944, 0.03243, 0.0077), Vector: |
-Components
#1: Protein | Mass: 53977.125 Da / Num. of mol.: 2 / Fragment: RESIDUES 62-554 / Source method: isolated from a natural source Source: (natural) GLUCONACETOBACTER DIAZOTROPHICUS (bacteria) Strain: SRT4 / References: UniProt: Q43998, levansucrase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 58.4 % |
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Crystal grow | pH: 5.6 Details: 0.5M AS, 30% ETHANOL, 0.1M NA-CITRATE PH5.6, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→51.98 Å / Num. obs: 48568 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OYG Resolution: 2.5→105.41 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 21.154 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.263 / 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: 24.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→105.41 Å
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Refine LS restraints |
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