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- PDB-8hw3: Limosilactobacillus reuteri N1 GtfB-acarbose -

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Basic information

Entry
Database: PDB / ID: 8hw3
TitleLimosilactobacillus reuteri N1 GtfB-acarbose
Componentsdextransucrase
KeywordsTRANSFERASE / glucanotransferase / carbohydrate-active enzyme
Function / homologyGlycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / Glycoside hydrolase superfamily / hydrolase activity / beta-acarbose / dextransucrase
Function and homology information
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsDong, J.J. / Bai, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32072268 China
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Insights into the Structure-Function Relationship of GH70 GtfB alpha-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized ...Title: Insights into the Structure-Function Relationship of GH70 GtfB alpha-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized Limosilactobacillus reuteri N1 GtfB Enzyme.
Authors: Dong, J. / Bai, Y. / Wang, Q. / Chen, Q. / Li, X. / Wang, Y. / Ji, H. / Meng, X. / Pijning, T. / Svensson, B. / Dijkhuizen, L. / Abou Hachem, M. / Jin, Z.
History
DepositionDec 28, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)187,5099
Polymers184,7882
Non-polymers2,7207
Water2,252125
1
A: dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7084
Polymers92,3941
Non-polymers1,3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8005
Polymers92,3941
Non-polymers1,4064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.770, 100.620, 106.670
Angle α, β, γ (deg.)90.00, 108.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein dextransucrase / N1 GtfB


Mass: 92394.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus reuteri (bacteria) / Gene: FOL80_07450 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A848PDI7, 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.: 4 / Source method: obtained synthetically / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 4% v/v MPD, 0.1 M Citric acid pH 3.5, 20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Aug 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.66→47.11 Å / Num. obs: 58618 / % possible obs: 99 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.2
Reflection shellResolution: 2.66→2.73 Å / Rmerge(I) obs: 0.501 / Num. unique obs: 4439

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→47.11 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.194 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 1.26 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26217 2965 5.1 %RANDOM
Rwork0.21205 ---
obs0.21456 55652 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.109 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å20 Å20.28 Å2
2--0.31 Å20 Å2
3----3.6 Å2
Refinement stepCycle: 1 / Resolution: 2.66→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12914 0 184 125 13223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01913399
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211942
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9418229
X-RAY DIFFRACTIONr_angle_other_deg0.7852.99127458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5551652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.88125.64688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.277152068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7771546
X-RAY DIFFRACTIONr_chiral_restr0.0720.22007
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023138
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_it1.8283.4686614
X-RAY DIFFRACTIONr_mcbond_other1.8283.4676613
X-RAY DIFFRACTIONr_mcangle_it3.0975.1978264
X-RAY DIFFRACTIONr_mcangle_other3.0975.1988265
X-RAY DIFFRACTIONr_scbond_it1.823.6736783
X-RAY DIFFRACTIONr_scbond_other1.823.6746781
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0025.4589965
X-RAY DIFFRACTIONr_long_range_B_refined5.72540.87915383
X-RAY DIFFRACTIONr_long_range_B_other5.68740.89515368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28681 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 214 -
Rwork0.304 3982 -
obs--97.45 %

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