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- PDB-8hwk: Limosilactobacillus reuteri N1 GtfB-maltohexaose -

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Basic information

Entry
Database: PDB / ID: 8hwk
TitleLimosilactobacillus reuteri N1 GtfB-maltohexaose
Componentsdextransucrase
KeywordsTRANSFERASE / glucanotransferase / carbohydrate-active enzyme
Function / homology
Function and homology information


dextransucrase / glucan biosynthetic process / glucosyltransferase activity / hydrolase activity
Similarity search - Function
Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-maltohexaose / CITRIC ACID / DI(HYDROXYETHYL)ETHER / dextransucrase
Similarity search - Component
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 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 30, 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)187,41210
Polymers184,7882
Non-polymers2,6248
Water1,74797
1
A: dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7065
Polymers92,3941
Non-polymers1,3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dextransucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7065
Polymers92,3941
Non-polymers1,3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.150, 101.188, 106.791
Angle α, β, γ (deg.)90.00, 108.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein dextransucrase / N1 GtfB enzyme


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 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 990.860 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: oligosaccharide / References: alpha-maltohexaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 103 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid pH 3.5, 14% PEG 1000

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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: Sep 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→23.74 Å / Num. obs: 46063 / % possible obs: 99.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.189 / Net I/σ(I): 5.4
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.473 / Num. unique obs: 4479

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→23.74 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.868 / SU B: 17.336 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26078 2323 5 %RANDOM
Rwork0.21469 ---
obs0.21701 43700 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.117 Å2
Baniso -1Baniso -2Baniso -3
1-4.33 Å2-0 Å21.53 Å2
2---1.82 Å20 Å2
3----2.89 Å2
Refinement stepCycle: 1 / Resolution: 2.9→23.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12914 0 176 97 13187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213383
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211918
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.94718226
X-RAY DIFFRACTIONr_angle_other_deg0.966327422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75551652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32725.731684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.431152068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4421546
X-RAY DIFFRACTIONr_chiral_restr0.1450.22000
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023134
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_it1.8193.096614
X-RAY DIFFRACTIONr_mcbond_other1.8183.096613
X-RAY DIFFRACTIONr_mcangle_it3.1034.638264
X-RAY DIFFRACTIONr_mcangle_other3.1034.6318265
X-RAY DIFFRACTIONr_scbond_it1.6773.2376766
X-RAY DIFFRACTIONr_scbond_other1.6773.2376766
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8734.8229960
X-RAY DIFFRACTIONr_long_range_B_refined5.09836.11615358
X-RAY DIFFRACTIONr_long_range_B_other5.09736.12715351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28303 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 157 -
Rwork0.265 3177 -
obs--97.91 %

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