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- PDB-5jbd: 4,6-alpha-glucanotransferase GTFB from Lactobacillus reuteri 121 -

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Basic information

Entry
Database: PDB / ID: 5jbd
Title4,6-alpha-glucanotransferase GTFB from Lactobacillus reuteri 121
ComponentsInactive glucansucrase
KeywordsTRANSFERASE / 4 / 6-alpha-glucanotransferase / starch conversion / GH70
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glucansucrase / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / dextransucrase
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPijning, T. / Dijkstra, B.W. / Bai, Y. / Gangoiti-Munecas, J. / Dijkhuizen, L.
Funding support China, Netherlands, 2items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CCC Research Netherlands
Citation
Journal: Structure / Year: 2017
Title: Crystal Structure of 4,6-alpha-Glucanotransferase Supports Diet-Driven Evolution of GH70 Enzymes from alpha-Amylases in Oral Bacteria.
Authors: Bai, Y. / Gangoiti, J. / Dijkstra, B.W. / Dijkhuizen, L. / Pijning, T.
#1: Journal: J.Agric.Food Chem. / Year: 2016
Title: Lactobacillus reuteri Strains Convert Starch and Maltodextrins into Homoexopolysaccharides Using an Extracellular and Cell-Associated 4,6-alpha-Glucanotransferase
Authors: Bai, Y. / Boger, M. / van der Kaaij, R.M. / Woortman, A.J.J. / Pijning, T. / van Leeuwen, S.S. / Lammerts van Bueren, A. / Dijkhuizen, L.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inactive glucansucrase
B: Inactive glucansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,75723
Polymers199,0192
Non-polymers1,73921
Water23,1131283
1
A: Inactive glucansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,37811
Polymers99,5091
Non-polymers86910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inactive glucansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,37912
Polymers99,5091
Non-polymers87011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.244, 57.852, 150.701
Angle α, β, γ (deg.)90.00, 114.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2371-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 761 - 1613 / Label seq-ID: 29 - 881

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inactive glucansucrase


Mass: 99509.398 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) / Variant (production host): star / References: UniProt: Q5SBM0, dextransucrase

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Non-polymers , 6 types, 1304 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1283 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG3350, NaCl, (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 4, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.8→45.83 Å / Num. obs: 158306 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 1.6 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3KLK domains A, B, C, IV

3klk


Resolution: 1.8→45.83 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.108 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 7949 5 %RANDOM
Rwork0.17732 ---
obs0.17883 150356 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 30.833 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å21.04 Å2
2---1.85 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.8→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13364 0 106 1283 14753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213785
X-RAY DIFFRACTIONr_bond_other_d0.0040.0212471
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.93618743
X-RAY DIFFRACTIONr_angle_other_deg1.06328610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9551725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71925.906723
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11152194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5561550
X-RAY DIFFRACTIONr_chiral_restr0.0740.22024
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216400
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023326
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2491.8676866
X-RAY DIFFRACTIONr_mcbond_other1.2351.8656860
X-RAY DIFFRACTIONr_mcangle_it1.8352.7918581
X-RAY DIFFRACTIONr_mcangle_other1.8362.7918582
X-RAY DIFFRACTIONr_scbond_it1.9032.0896919
X-RAY DIFFRACTIONr_scbond_other1.9022.0896919
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9683.04210157
X-RAY DIFFRACTIONr_long_range_B_refined5.20916.05616730
X-RAY DIFFRACTIONr_long_range_B_other5.09815.49716145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 102602 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 536 -
Rwork0.325 10750 -
obs--96.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32350.1543-0.21970.2946-0.15040.7781-0.01770.08730.1115-0.07720.05110.0064-0.0087-0.0206-0.03330.0794-0.0180.06740.06320.03010.119232.61236.23218.053
20.376-0.1081-0.22350.34290.15150.4994-0.0030.02140.0457-0.01670.01290.041-0.0489-0.0248-0.00990.0534-0.00320.02750.01380.01830.0594-7.7225.98551.246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A761 - 1614
2X-RAY DIFFRACTION2B761 - 1615

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