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Yorodumi- PDB-7p38: 4,6-alpha-glucanotransferase GtfB from Limosilactobacillus reuter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p38 | ||||||
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Title | 4,6-alpha-glucanotransferase GtfB from Limosilactobacillus reuteri NCC 2613 | ||||||
Components | Dextransucrase | ||||||
Keywords | TRANSFERASE / 4 / 6-alpha-transglycosylation / GtfB / Starch conversion | ||||||
Function / homology | dextransucrase activity / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / Glycoside hydrolase superfamily / Dextransucrase Function and homology information | ||||||
Biological species | Lactobacillus reuteri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Pijning, T. / te Poele, E. / Gangoiti, J. / Boerner, T. / Dijkhuizen, L. | ||||||
Citation | Journal: J.Agric.Food Chem. / Year: 2021 Title: Insights into Broad-Specificity Starch Modification from the Crystal Structure of Limosilactobacillus Reuteri NCC 2613 4,6-alpha-Glucanotransferase GtfB. Authors: Pijning, T. / Gangoiti, J. / Te Poele, E.M. / Borner, T. / Dijkhuizen, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p38.cif.gz | 644.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p38.ent.gz | 526.9 KB | Display | PDB format |
PDBx/mmJSON format | 7p38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/7p38 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/7p38 | HTTPS FTP |
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-Related 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 domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 446 - 1277 / Label seq-ID: 50 - 881
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-Components
#1: Protein | Mass: 97834.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Z2RUH3, dextransucrase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.73 Å3/Da / Density % sol: 54.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.4-1.7 M (NH4)2SO4, 0.1 M Bis-Tris-HCl, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.695→47.24 Å / Num. obs: 59781 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.955 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.094 / Rrim(I) all: 0.273 / Net I/σ(I): 6.1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Obtained from Phyre homology modeling Resolution: 2.7→47.24 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.886 / SU B: 37.437 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.246 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.95 Å2 / Biso mean: 37.994 Å2 / Biso min: 2.63 Å2
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Refinement step | Cycle: final / Resolution: 2.7→47.24 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 27521 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.7→2.765 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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