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

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Basic information

Entry
Database: PDB / ID: 5jbe
Title4,6-alpha-glucanotransferase GTFB from Lactobacillus reuteri 121 complexed with an isomalto-maltopentasaccharide
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
alpha-maltose / ACETATE ION / beta-D-glucopyranose / dextransucrase
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsPijning, T. / Dijkstra, B.W. / Bai, Y. / Gangoiti-Munecas, J. / Dijkhuizen, L.
Funding support China, Netherlands, 2items
OrganizationGrant numberCountry
China 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: Journal of Agricultural and Food Chemistry / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)192,80518
Polymers189,8062
Non-polymers2,99916
Water11,223623
1
A: Inactive glucansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3589
Polymers94,9031
Non-polymers1,4558
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inactive glucansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4469
Polymers94,9031
Non-polymers1,5438
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.441, 58.324, 151.410
Angle α, β, γ (deg.)90.000, 114.250, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1890-

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: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 761 - 1614 / Label seq-ID: 1 - 854

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: 94903.055 Da / Num. of mol.: 2 / Fragment: GTFB-dNdV
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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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 635 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG3350, NaCl, (NH4)2)SO4

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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: 2.1→46.16 Å / Num. obs: 102167 / % possible obs: 99.4 % / Redundancy: 4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.071 / Rrim(I) all: 0.145 / Net I/σ(I): 7.7 / Num. measured all: 406237 / Scaling rejects: 3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.818 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.75 Å46.16 Å
Translation6.75 Å46.16 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASER2.5.1phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 3KLK domains A, B, C, IV

3klk


Resolution: 2.1→46.16 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.644 / SU ML: 0.185 / SU R Cruickshank DPI: 0.2655 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.195 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 5150 5 %RANDOM
Rwork0.2064 ---
obs0.2079 97017 99.16 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.41 Å2 / Biso mean: 39.018 Å2 / Biso min: 18.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å2-0 Å21.01 Å2
2---3.06 Å20 Å2
3---1.14 Å2
Refinement stepCycle: final / Resolution: 2.1→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13356 0 193 623 14172
Biso mean--55.09 36.2 -
Num. residues----1708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213820
X-RAY DIFFRACTIONr_bond_other_d0.0040.0212445
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.94718812
X-RAY DIFFRACTIONr_angle_other_deg1.1193.00528582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06951706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54325.866716
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.746152180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1921550
X-RAY DIFFRACTIONr_chiral_restr0.0760.22069
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216274
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023304
X-RAY DIFFRACTIONr_mcbond_it0.5311.46836
X-RAY DIFFRACTIONr_mcbond_other0.521.3966829
X-RAY DIFFRACTIONr_mcangle_it0.8972.0928534
Refine LS restraints NCS

Ens-ID: 1 / Number: 101684 / 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: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 356 -
Rwork0.311 7107 -
all-7463 -
obs--98.76 %
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)
10.74560.1688-0.08890.2657-0.09470.7913-0.0364-0.06390.1109-0.02640.00780.0031-0.06030.02040.02860.03170.01330.01230.524-0.02930.0387349.196-22.455294.113
20.2981-0.074-0.15980.22380.11720.4257-0.0263-0.17960.02860.03140.03960.03880.0061-0.0661-0.01330.02690.03720.01590.74610.0090.0209308.93-32.791327.441
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A761 - 1614
2X-RAY DIFFRACTION2B761 - 1614

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