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- PDB-3kll: Crystal structure of Lactobacillus reuteri N-terminally truncated... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kll | |||||||||
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Title | Crystal structure of Lactobacillus reuteri N-terminally truncated glucansucrase GTF180-maltose complex | |||||||||
![]() | Glucansucrase | |||||||||
![]() | TRANSFERASE / glucansucrase-maltose complex / multidomain protein / Glycosyltransferase | |||||||||
Function / homology | ![]() dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Vujicic-Zagar, A. / Pijning, T. / Kralj, S. / Eeuwema, W. / Dijkhuizen, L. / Dijkstra, B.W. | |||||||||
![]() | ![]() Title: Crystal structure of a 117 kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes Authors: Vujicic-Zagar, A. / Pijning, T. / Kralj, S. / Lopez, C.A. / Eeuwema, W. / Dijkhuizen, L. / Dijkstra, B.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.9 KB | Display | ![]() |
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PDB format | ![]() | 182.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 66.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hz3C ![]() 3klkSC ![]() 3hq3 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: 117767.336 Da / Num. of mol.: 1 Fragment: N-terminally truncated GTF180, UNP residues 742-1772 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | THE CONFLICT F1674L MAY DUE TO PCR ERROR. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 3350, BIS-TRIS propane buffer, CaCl2, pH 6.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.997→38.747 Å / Num. obs: 75992 / % possible obs: 97.5 % / Redundancy: 2.4 % / Rsym value: 0.053 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 10726 / Rsym value: 0.171 / % possible all: 94 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3KLK Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 3.576 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 233.6 Å2 / Biso mean: 29.568 Å2 / Biso min: 13.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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