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- PDB-9j4l: Crystal structure of GH9l Inulin fructotransferases (IFTase) -

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Basic information

Entry
Database: PDB / ID: 9j4l
TitleCrystal structure of GH9l Inulin fructotransferases (IFTase)
ComponentsDFA-III-forming inulin fructotransferase
KeywordsCARBOHYDRATE / fructotransferases
Function / homology
Function and homology information


inulin fructotransferase (DFA-III-forming) / inulin fructotransferase (DFA-III-forming) activity / transferase activity
Similarity search - Function
Inulin fructotransferase, beta helix repeat / Beta helix repeat of Inulin fructotransferase / Periplasmic copper-binding protein NosD, beta helix domain / Periplasmic copper-binding protein (NosD) / Pectin lyase fold / Pectin lyase fold/virulence factor / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
DFA-III-forming inulin fructotransferase
Similarity search - Component
Biological speciesPaenarthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.15 Å
AuthorsChen, G. / Wang, Z.X. / Yang, Y.Q. / Li, Y.G. / Zhang, T. / Ouyang, S.Y. / Zhang, L. / Chen, Y. / Ruan, X.L. / Miao, M.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of Sciences2018YFC1602101 China
National Natural Science Foundation of China (NSFC)31972029 China
National Natural Science Foundation of China (NSFC)31770948 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Elucidation of the mechanism underlying the sequential catalysis of inulin by fructotransferase.
Authors: Chen, G. / Wang, Z.X. / Yang, Y. / Li, Y. / Zhang, T. / Ouyang, S. / Zhang, L. / Chen, Y. / Ruan, X. / Miao, M.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DFA-III-forming inulin fructotransferase
B: DFA-III-forming inulin fructotransferase
C: DFA-III-forming inulin fructotransferase


Theoretical massNumber of molelcules
Total (without water)129,6433
Polymers129,6433
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-66 kcal/mol
Surface area34310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.680, 167.680, 85.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DFA-III-forming inulin fructotransferase


Mass: 43214.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter aurescens (bacteria) / Gene: ift / Production host: Escherichia coli (E. coli)
References: UniProt: F8QV43, inulin fructotransferase (DFA-III-forming)

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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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris (pH 8.5),and 25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→19.95 Å / Num. obs: 73905 / % possible obs: 98.5 % / Redundancy: 4.7 % / CC1/2: 0.993 / Net I/σ(I): 9.58
Reflection shellResolution: 2.15→2.21 Å / Num. unique obs: 9303 / CC1/2: 0.512

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
RESOLVEmodel building
HKL-3000data scaling
HKL-3000data reduction
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→9.62 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: FREE R-VALUE / ESU R: 0.233 / ESU R Free: 0.184
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.233 3724 5.039 %
Rwork0.205 70181 -
all0.206 --
obs-73905 99.038 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.252 Å2
Baniso -1Baniso -2Baniso -3
1-0.026 Å20.013 Å20 Å2
2--0.026 Å2-0 Å2
3----0.085 Å2
Refinement stepCycle: LAST / Resolution: 2.15→9.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9080 0 0 0 9080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0139272
X-RAY DIFFRACTIONr_bond_other_d0.0360.0158649
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.63912625
X-RAY DIFFRACTIONr_angle_other_deg2.4121.57819889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.04451206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36922.398467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.791151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3671560
X-RAY DIFFRACTIONr_chiral_restr0.1390.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210785
X-RAY DIFFRACTIONr_gen_planes_other0.0140.022117
X-RAY DIFFRACTIONr_nbd_refined0.2050.21617
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2430.28669
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24463
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.24641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2203
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.213
X-RAY DIFFRACTIONr_nbd_other0.2570.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0820.21
X-RAY DIFFRACTIONr_mcbond_it2.032.2184836
X-RAY DIFFRACTIONr_mcbond_other2.0292.2184835
X-RAY DIFFRACTIONr_mcangle_it2.7373.3186038
X-RAY DIFFRACTIONr_mcangle_other2.7373.3186039
X-RAY DIFFRACTIONr_scbond_it3.1172.3684436
X-RAY DIFFRACTIONr_scbond_other3.1162.3684437
X-RAY DIFFRACTIONr_scangle_it3.9663.4756587
X-RAY DIFFRACTIONr_scangle_other3.9663.4756588
X-RAY DIFFRACTIONr_lrange_it4.69625.9849395
X-RAY DIFFRACTIONr_lrange_other4.69725.9859396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.2050.3332380.2894727X-RAY DIFFRACTION91.2852
2.205-2.2650.2672560.2574914X-RAY DIFFRACTION97.8796
2.265-2.330.32800.2474868X-RAY DIFFRACTION99.8061
2.33-2.40.2952370.2464761X-RAY DIFFRACTION100
2.4-2.4780.2512490.2334622X-RAY DIFFRACTION100
2.478-2.5630.262180.2224464X-RAY DIFFRACTION100
2.563-2.6590.2542190.2334342X-RAY DIFFRACTION99.9781
2.659-2.7650.2482230.2174153X-RAY DIFFRACTION100
2.765-2.8850.2452110.2123968X-RAY DIFFRACTION100
2.885-3.0230.252030.213805X-RAY DIFFRACTION99.9751
3.023-3.1830.2382200.1993636X-RAY DIFFRACTION99.9741
3.183-3.370.2111950.2013444X-RAY DIFFRACTION100
3.37-3.5960.2181850.183225X-RAY DIFFRACTION99.9414
3.596-3.8730.1951650.1753036X-RAY DIFFRACTION100
3.873-4.2270.1981380.1742812X-RAY DIFFRACTION100
4.227-4.70.1671290.1542577X-RAY DIFFRACTION99.8524
4.7-5.3770.1961360.1662263X-RAY DIFFRACTION99.9583
5.377-6.4690.261910.2211977X-RAY DIFFRACTION100
6.469-8.7030.21660.2031575X-RAY DIFFRACTION99.9391
8.703-9.620.21650.1971013X-RAY DIFFRACTION99.7225

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