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

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Basic information

Entry
Database: PDB / ID: 8xvp
TitleCrystal structure of inulosucrase from Lactobacillus reuteri 121
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
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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)173,97410
Polymers173,5502
Non-polymers4258
Water7,206400
1
A: Inulosucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9875
Polymers86,7751
Non-polymers2124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area19160 Å2
MethodPISA
2
B: Inulosucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9875
Polymers86,7751
Non-polymers2124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.910, 98.690, 139.490
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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M Tris pH 8.5 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.23981 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23981 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 68149 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.039 / Rrim(I) all: 0.141 / Χ2: 1.06 / Net I/σ(I): 13.8
Reflection shellResolution: 1.98→2.02 Å / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 1.246 / Num. measured all: 53823 / Num. unique obs: 4528 / CC1/2: 0.794 / Rpim(I) all: 0.373 / Rrim(I) all: 1.302 / Χ2: 0.85 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→49.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.497 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24456 3356 4.9 %RANDOM
Rwork0.20044 ---
obs0.20265 64716 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.306 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å2-0 Å2-0 Å2
2---2.51 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 1.98→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8026 0 18 400 8444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028265
X-RAY DIFFRACTIONr_bond_other_d0.0010.027485
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.93111230
X-RAY DIFFRACTIONr_angle_other_deg0.778317199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59551025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88725.99419
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.582151314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8071526
X-RAY DIFFRACTIONr_chiral_restr0.0810.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021904
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_it2.2293.5254113
X-RAY DIFFRACTIONr_mcbond_other2.2273.5254106
X-RAY DIFFRACTIONr_mcangle_it3.2255.2785124
X-RAY DIFFRACTIONr_mcangle_other3.2255.2785125
X-RAY DIFFRACTIONr_scbond_it2.3583.7324152
X-RAY DIFFRACTIONr_scbond_other2.3573.7324152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6115.56106
X-RAY DIFFRACTIONr_long_range_B_refined5.27541.8849842
X-RAY DIFFRACTIONr_long_range_B_other5.25241.7869736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 16927 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.98→2.029 Å
RfactorNum. reflection% reflection
Rfree0.313 255 -
Rwork0.29 4721 -
obs--99.8 %

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