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- PDB-5ngy: Crystal structure of Leuconostoc citreum NRRL B-1299 dextransucra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ngy | |||||||||
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Title | Crystal structure of Leuconostoc citreum NRRL B-1299 dextransucrase DSR-M | |||||||||
![]() | DSR-M glucansucrase inactive mutant E715Q | |||||||||
![]() | TRANSFERASE / dextransucrase / dextran / sugar binding protein | |||||||||
Function / homology | ![]() dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Claverie, M. / Cioci, G. / Remaud-simeon, M. / Moulis, C. / Tranier, S. / Vuillemin, M. | |||||||||
![]() | ![]() Title: Investigations on the Determinants Responsible for Low Molar Mass Dextran Formation by DSR-M Dextransucrase Authors: Claverie, M. / Cioci, G. / Vuillemin, M. / Monties, N. / Roblin, P. / Lippens, G. / Remaud-simeon, M. / Moulis, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 932.1 KB | Display | ![]() |
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PDB format | ![]() | 761.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lfcSC ![]() 5o8lC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 143976.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-PR / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.7 % / Description: thin rod |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG3350, 0.2M KSCN, 0.1 Pr(III)acetate, BIS-TRIS pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 15, 2016 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→50 Å / Num. obs: 34388 / % possible obs: 98.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 44.5 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.1 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 3.7→3.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4910 / CC1/2: 0.822 / Rpim(I) all: 0.284 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5lfc Resolution: 3.7→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / SU B: 80.89 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.681 / 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: 62.15 Å2
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Refinement step | Cycle: 1 / Resolution: 3.7→50 Å
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Refine LS restraints |
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