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- PDB-8xvq: Crystal structure of inulosucrase from Lactobacillus reuteri 121 ... -

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Basic information

Entry
Database: PDB / ID: 8xvq
TitleCrystal structure of inulosucrase from Lactobacillus reuteri 121 in complex with fructose
ComponentsInulosucrase
KeywordsHYDROLASE / Glycoside hydrolase 68 enzyme
Function / homology
Function and homology information


inulosucrase / inulosucrase activity / levansucrase activity / carbohydrate utilization / extracellular region / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 68 / Levansucrase/Invertase / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
beta-D-fructofuranose / Inulosucrase
Similarity search - Component
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsNi, D. / Hou, X. / Cheng, M. / Xu, W. / Rao, Y. / Mu, W.
Funding support China, 3items
OrganizationGrant numberCountry
Other private2023YFF1103600 China
National Natural Science Foundation of China (NSFC)22308118 China
Other privateBK20231045 China
CitationJournal: To Be Published
Title: Structure-guided tunnel engineering to reveal the molecular basis of sugar chain extension of inulosucrase
Authors: Ni, D. / Hou, X. / Cheng, M. / Xu, W. / Rao, Y. / Mu, W.
History
DepositionJan 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inulosucrase
B: Inulosucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,0708
Polymers173,5502
Non-polymers5216
Water6,035335
1
A: Inulosucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0354
Polymers86,7751
Non-polymers2603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area19620 Å2
MethodPISA
2
B: Inulosucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0354
Polymers86,7751
Non-polymers2603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.240, 99.920, 153.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Inulosucrase / Levansucrase


Mass: 86774.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus reuteri (bacteria) / Gene: inu, DPH67_05265
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8GP32, inulosucrase
#2: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.55 Å3/Da / Density % sol: 20.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 59439 / % possible obs: 98.8 % / Redundancy: 11.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.035 / Rrim(I) all: 0.123 / Χ2: 0.94 / Net I/σ(I): 17
Reflection shellResolution: 2.14→2.2 Å / % possible obs: 89.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.346 / Num. measured all: 25239 / Num. unique obs: 4085 / CC1/2: 0.944 / Rpim(I) all: 0.143 / Rrim(I) all: 0.375 / Χ2: 0.68 / Net I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→47.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.494 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22713 3015 5.1 %RANDOM
Rwork0.17762 ---
obs0.1801 56361 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å2-0 Å2
2---0.6 Å20 Å2
3---1.49 Å2
Refinement stepCycle: 1 / Resolution: 2.14→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8115 0 28 335 8478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028354
X-RAY DIFFRACTIONr_bond_other_d0.0010.027563
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.93311356
X-RAY DIFFRACTIONr_angle_other_deg0.745317385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61151037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86325.976420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.146151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3071526
X-RAY DIFFRACTIONr_chiral_restr0.0750.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021920
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_it1.2252.3934158
X-RAY DIFFRACTIONr_mcbond_other1.2232.3944151
X-RAY DIFFRACTIONr_mcangle_it2.0033.5855182
X-RAY DIFFRACTIONr_mcangle_other2.0033.5855183
X-RAY DIFFRACTIONr_scbond_it1.4422.5374196
X-RAY DIFFRACTIONr_scbond_other1.4422.5374196
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3413.7326174
X-RAY DIFFRACTIONr_long_range_B_refined3.72528.0959757
X-RAY DIFFRACTIONr_long_range_B_other3.66227.9719662
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 223 -
Rwork0.195 3621 -
obs--87.8 %

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