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

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Basic information

Entry
Database: PDB / ID: 8xvr
TitleCrystal structure of inulosucrase from Lactobacillus reuteri 121 mutant R544W
ComponentsGlycoside hydrolase family 68 protein
KeywordsHYDROLASE / Glycoside hydrolase 68 enzyme
Function / homologyDI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsNi, D. / Hou, X. / Cheng, M. / Xu, W. / Rao, Y. / Mu, W.
Funding support China, 3items
OrganizationGrant numberCountry
Other private2023YFF1103600
National Natural Science Foundation of China (NSFC)22308118 China
Other privateBK20231045
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

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Assembly

Deposited unit
A: Glycoside hydrolase family 68 protein
B: Glycoside hydrolase family 68 protein
C: Glycoside hydrolase family 68 protein
D: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,55743
Polymers260,9424
Non-polymers2,61539
Water17,925995
1
A: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,95610
Polymers65,2351
Non-polymers7219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,84211
Polymers65,2351
Non-polymers60710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,99613
Polymers65,2351
Non-polymers76112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase family 68 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7629
Polymers65,2351
Non-polymers5278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.570, 132.080, 121.780
Angle α, β, γ (deg.)90.00, 110.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycoside hydrolase family 68 protein


Mass: 65235.375 Da / Num. of mol.: 4 / Mutation: R544W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus reuteri (bacteria) / Gene: DPAN417_05420
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6N1ER42

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Non-polymers , 6 types, 1034 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 995 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3000 200 mM Sodium acetate Acetic acid pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.44→41.59 Å / Num. obs: 100399 / % possible obs: 98.4 % / Redundancy: 6.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.061 / Rrim(I) all: 0.159 / Χ2: 0.99 / Net I/σ(I): 11
Reflection shellResolution: 2.44→2.48 Å / % possible obs: 82.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.529 / Num. measured all: 20006 / Num. unique obs: 4148 / CC1/2: 0.837 / Rpim(I) all: 0.259 / Rrim(I) all: 0.592 / Χ2: 0.92 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→41.59 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.789 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21558 4965 4.9 %RANDOM
Rwork0.17964 ---
obs0.18144 95396 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.375 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.04 Å2
2---0.24 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.44→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16338 0 157 995 17490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216903
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215370
X-RAY DIFFRACTIONr_angle_refined_deg1.491.93322913
X-RAY DIFFRACTIONr_angle_other_deg0.804335328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94852087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93226845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.178152669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4441549
X-RAY DIFFRACTIONr_chiral_restr0.0840.22482
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023866
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_it1.6152.218359
X-RAY DIFFRACTIONr_mcbond_other1.6092.218346
X-RAY DIFFRACTIONr_mcangle_it2.5963.30910417
X-RAY DIFFRACTIONr_mcangle_other2.5963.30910418
X-RAY DIFFRACTIONr_scbond_it1.9232.4038544
X-RAY DIFFRACTIONr_scbond_other1.9232.4038544
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1073.49912493
X-RAY DIFFRACTIONr_long_range_B_refined4.63325.68519873
X-RAY DIFFRACTIONr_long_range_B_other4.56525.63119593
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A172860.05
12B172860.05
21A173070.06
22C173070.06
31A176010.04
32D176010.04
41B178180.04
42C178180.04
51B172770.06
52D172770.06
61C172870.06
62D172870.06
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 293 -
Rwork0.239 6029 -
obs--84.15 %

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