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- PDB-7p39: 4,6-alpha-glucanotransferase GtfB from Limosilactobacillus reuter... -

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Basic information

Entry
Database: PDB / ID: 7p39
Title4,6-alpha-glucanotransferase GtfB from Limosilactobacillus reuteri NCC 2613 complexed with acarbose
ComponentsDextransucrase
KeywordsTRANSFERASE / 4 / 6-alpha-transglycosylation / GtfB / Starch conversion
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-acarbose / dextransucrase
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsPijning, T. / te Poele, E. / Gangoiti, J. / Boerner, T. / Dijkhuizen, L.
CitationJournal: 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
DepositionJul 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 17, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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: Dextransucrase
B: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,1357
Polymers195,6682
Non-polymers1,4675
Water34219
1
A: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6164
Polymers97,8341
Non-polymers7823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5203
Polymers97,8341
Non-polymers6862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.219, 133.806, 147.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / 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: _ / Auth seq-ID: 446 - 1277 / Label seq-ID: 50 - 881

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

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Components

#1: Protein Dextransucrase / Sucrose 6-glucosyltransferase


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: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-acarbose
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.4-1.7 M (NH4)2SO4, 0.1 M Bis-Tris-HCl, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→49.29 Å / Num. obs: 46821 / % possible obs: 98.3 % / Redundancy: 9.1 % / CC1/2: 0.975 / Rmerge(I) obs: 0.43 / Rpim(I) all: 0.141 / Rrim(I) all: 0.454 / Net I/σ(I): 3.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-391.6484085645260.6390.5511.7441.198.9
11.23-49.298.30.11673398800.9960.040.1238.395.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.96 Å47.16 Å
Translation5.96 Å47.16 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Obtained from Phyre homology modeling

Resolution: 2.9→49.29 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.857 / SU B: 31.723 / SU ML: 0.535 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3146 2250 4.8 %RANDOM
Rwork0.2932 ---
obs0.2943 44476 97.75 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 101.97 Å2 / Biso mean: 41.72 Å2 / Biso min: 4.93 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å2-0 Å20 Å2
2--5.63 Å2-0 Å2
3----2.65 Å2
Refinement stepCycle: final / Resolution: 2.9→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13022 0 95 19 13136
Biso mean--48.53 15.18 -
Num. residues----1664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211398
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.94118276
X-RAY DIFFRACTIONr_angle_other_deg0.917326620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09851662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.00925.652690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.568152078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2821548
X-RAY DIFFRACTIONr_chiral_restr0.0660.21995
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022650
Refine LS restraints NCS

Ens-ID: 1 / Number: 55432 / 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: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 149 -
Rwork0.426 3254 -
all-3403 -
obs--98.27 %

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