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- PDB-9j4k: Crystal structure of GH9l Inulinfructotransferases (IFTase) in co... -

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Basic information

Entry
Database: PDB / ID: 9j4k
TitleCrystal structure of GH9l Inulinfructotransferases (IFTase) in complex with GF2
ComponentsDFA-III-forming inulin fructotransferase
KeywordsCARBOHYDRATE / IFTase / catalytic pathway / HYDROLASE
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
1-kestose / DFA-III-forming inulin fructotransferase
Similarity search - Component
Biological speciesPaenarthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.201 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,6709
Polymers129,6433
Non-polymers3,0276
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20410 Å2
ΔGint4 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.580, 167.580, 85.478
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)
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: 1-kestose
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-2/a1-b2_b1-c2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate monohydrate 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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 69363 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.48
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 3469

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→48.423 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.527 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.2 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1843 3508 5.062 %
Rwork0.1462 65788 -
all0.148 --
obs-69296 99.885 %
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: 33.899 Å2
Baniso -1Baniso -2Baniso -3
1--0.018 Å2-0.009 Å2-0 Å2
2---0.018 Å20 Å2
3---0.059 Å2
Refinement stepCycle: LAST / Resolution: 2.201→48.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9081 0 204 547 9832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139519
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158844
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.6712963
X-RAY DIFFRACTIONr_angle_other_deg1.2211.60320364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.20351212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82422.215474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.129151425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.721563
X-RAY DIFFRACTIONr_chiral_restr0.0550.21317
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022133
X-RAY DIFFRACTIONr_nbd_refined0.1850.21639
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.28760
X-RAY DIFFRACTIONr_nbtor_refined0.1490.24546
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.24532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2583
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.214
X-RAY DIFFRACTIONr_nbd_other0.2490.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.27
X-RAY DIFFRACTIONr_mcbond_it1.5693.4634839
X-RAY DIFFRACTIONr_mcbond_other1.5673.4634838
X-RAY DIFFRACTIONr_mcangle_it2.215.1926045
X-RAY DIFFRACTIONr_mcangle_other2.215.1936046
X-RAY DIFFRACTIONr_scbond_it1.993.7494680
X-RAY DIFFRACTIONr_scbond_other1.9883.7494680
X-RAY DIFFRACTIONr_scangle_it2.8895.5476915
X-RAY DIFFRACTIONr_scangle_other2.8895.5486916
X-RAY DIFFRACTIONr_lrange_it4.18442.0239924
X-RAY DIFFRACTIONr_lrange_other4.12441.7949837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.2580.192590.1384838X-RAY DIFFRACTION99.6286
2.258-2.320.182450.1354730X-RAY DIFFRACTION99.9197
2.32-2.3870.1992300.1454598X-RAY DIFFRACTION99.8759
2.387-2.4610.1952460.1434443X-RAY DIFFRACTION99.8935
2.461-2.5410.1992230.1444340X-RAY DIFFRACTION99.8468
2.541-2.630.1912290.1424161X-RAY DIFFRACTION99.8862
2.63-2.730.2121950.1614052X-RAY DIFFRACTION99.9294
2.73-2.8410.2152110.163914X-RAY DIFFRACTION99.9758
2.841-2.9670.2122070.1513703X-RAY DIFFRACTION99.8723
2.967-3.1120.21900.1563567X-RAY DIFFRACTION100
3.112-3.2810.1971800.153413X-RAY DIFFRACTION99.9722
3.281-3.4790.1881590.1473240X-RAY DIFFRACTION99.9706
3.479-3.7190.1721650.1443019X-RAY DIFFRACTION99.9686
3.719-4.0170.1641670.1382795X-RAY DIFFRACTION99.7642
4.017-4.40.171500.1352594X-RAY DIFFRACTION99.8544
4.4-4.9190.1461340.1142354X-RAY DIFFRACTION99.9197
4.919-5.6790.1921020.1542095X-RAY DIFFRACTION99.9545
5.679-6.9530.225950.1891772X-RAY DIFFRACTION100
6.953-9.8210.183790.1511381X-RAY DIFFRACTION100
9.821-48.4230.13420.173779X-RAY DIFFRACTION99.035

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