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- PDB-7dt1: The structure of Lactobacillus fermentum 4,6-alpha-Glucanotransferase -

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Basic information

Entry
Database: PDB / ID: 7dt1
TitleThe structure of Lactobacillus fermentum 4,6-alpha-Glucanotransferase
ComponentsDextransucrase
KeywordsTRANSFERASE / Glycoside Hydrolase Family 70 / U-course / 4 / 6-alpha-Glucanotransferase
Function / homologydextransucrase activity / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / Glycoside hydrolase superfamily / DI(HYDROXYETHYL)ETHER / Dextransucrase
Function and homology information
Biological speciesLimosilactobacillus fermentum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4300227139 Å
AuthorsYang, W.K. / Yong, Y.H. / Wu, L. / Chen, S. / Zhou, J.H. / Wu, J.
CitationJournal: Food Biosci / Year: 2022
Title: Characterization of a new 4,6-alpha-glucanotransferase from Limosilactobacillus fermentum NCC 3057 with ability of synthesizing low molecular mass isomalto-/maltopolysaccharide
Authors: Yang, W. / Sheng, L. / Chen, S. / Wang, L. / Su, L. / Wu, J.
History
DepositionJan 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dextransucrase
B: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,04465
Polymers234,8872
Non-polymers4,15763
Water20,8251156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-3 kcal/mol
Surface area63240 Å2
Unit cell
Length a, b, c (Å)99.830, 106.080, 106.020
Angle α, β, γ (deg.)90.000, 104.832, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dextransucrase / Sucrose 6-glucosyltransferase


Mass: 117443.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus fermentum (bacteria)
Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A1Z2RUD1, dextransucrase

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Non-polymers , 5 types, 1219 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.76 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M imidazole/hydrochloric acid buffer pH 8.5, 0.2 M calcium acetate , 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.43→48.73 Å / Num. obs: 80425 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.4393052473 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.4
Reflection shellResolution: 2.43→2.48 Å / Num. unique obs: 4541 / CC1/2: 0.827

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JBE

5jbe


Resolution: 2.4300227139→48.7263365866 Å / SU ML: 0.291604304582 / Cross valid method: FREE R-VALUE / σ(F): 1.34351629258 / Phase error: 29.4320367997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256481915017 3842 4.78861302224 %
Rwork0.193663259612 76390 -
obs0.196616983888 80232 99.5990317175 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.2621144871 Å2
Refinement stepCycle: LAST / Resolution: 2.4300227139→48.7263365866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13246 0 252 1156 14654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0070839702395613740
X-RAY DIFFRACTIONf_angle_d0.86570302099618588
X-RAY DIFFRACTIONf_chiral_restr0.0496951730492003
X-RAY DIFFRACTIONf_plane_restr0.004927897320862449
X-RAY DIFFRACTIONf_dihedral_angle_d12.62112322228077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.430023-2.46080.3297531081251330.2568465512342841X-RAY DIFFRACTION99.4981599197
2.4608-2.49320.3191052375671580.2379104828672783X-RAY DIFFRACTION99.6949152542
2.4932-2.52730.3012050673161200.2374779068412834X-RAY DIFFRACTION99.3609149008
2.5273-2.56340.3002120127771600.229146940922787X-RAY DIFFRACTION99.8306233062
2.5634-2.60170.2828405921141490.2266627451052804X-RAY DIFFRACTION99.5952782462
2.6017-2.64230.300191548481500.2270279633662827X-RAY DIFFRACTION99.6318607764
2.6423-2.68560.3070953560161340.2289017957832790X-RAY DIFFRACTION99.6252129472
2.6856-2.73190.3263056431511610.2263195137662827X-RAY DIFFRACTION99.6664442962
2.7319-2.78160.3176905236141610.2238188909092803X-RAY DIFFRACTION99.5967741935
2.7816-2.83510.3278434633041330.2315995649692814X-RAY DIFFRACTION99.7292724196
2.8351-2.8930.3110845090471260.2244693698322846X-RAY DIFFRACTION99.7650218194
2.893-2.95590.315500962881090.2034465350512840X-RAY DIFFRACTION99.6620479892
2.9559-3.02460.2339813206831410.2051881182362837X-RAY DIFFRACTION99.6986943421
3.0246-3.10030.2432629639861460.2041396817622829X-RAY DIFFRACTION99.6649916248
3.1003-3.18410.2696381246491540.2000454977122804X-RAY DIFFRACTION99.8986828774
3.1841-3.27770.2784868899131460.2072723941912813X-RAY DIFFRACTION99.8313090418
3.2777-3.38350.2716394138061430.2033950328722862X-RAY DIFFRACTION100
3.3835-3.50440.2461001477141460.201972195392827X-RAY DIFFRACTION99.8991935484
3.5044-3.64470.2521272997141550.1871480461262839X-RAY DIFFRACTION99.8998998999
3.6447-3.81050.2404628395681440.1694561769962824X-RAY DIFFRACTION99.865410498
3.8105-4.01130.2235770003511350.1605342368832833X-RAY DIFFRACTION99.865410498
4.0113-4.26250.214699352851230.155425573882884X-RAY DIFFRACTION100
4.2625-4.59140.179800509121490.1494241804572836X-RAY DIFFRACTION99.9330431871
4.5914-5.0530.2063373015191490.1553233693872866X-RAY DIFFRACTION99.9337089824
5.053-5.78310.264777672571470.1695115088892843X-RAY DIFFRACTION99.7997329773
5.7831-7.28220.2106394406971440.1895849626882876X-RAY DIFFRACTION99.8677248677
7.2822-48.72633658660.2271178226981260.1895155213392821X-RAY DIFFRACTION95.5577172503

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