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- PDB-9j4i: Crystal structure of GH9l Inulin fructotransferases (IFTase) in c... -

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Basic information

Entry
Database: PDB / ID: 9j4i
TitleCrystal structure of GH9l Inulin fructotransferases (IFTase) in compex with fruetosyl nystose (GF4)
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
DFA-III-forming inulin fructotransferase
Similarity search - Component
Biological speciesPaenarthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 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)135,28210
Polymers129,6433
Non-polymers5,6397
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25910 Å2
ΔGint98 kcal/mol
Surface area32170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.713, 167.713, 85.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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)-beta-D-fructofuranose-(2-1)-[alpha-D- ...beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-[alpha-D-glucopyranose-(1-2)]beta-D-fructofuranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DFrufb2-1[DGlcpa1-2]DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-2-2-2/a1-b2_b1-c2_c1-d2_d1-e2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-[alpha-D-glucopyranose-(1-2)]beta-D-fructofuranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1DFrufb2-1[DGlcpa1-2]DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-2-2/a1-b2_b1-c2_c1-d2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 53.88 %
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: 1.96→50 Å / Num. obs: 94026 / % possible obs: 96.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.2
Reflection shellResolution: 1.96→1.99 Å / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.277 / Num. unique obs: 4791

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→42.12 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18469 4693 5 %RANDOM
Rwork0.15864 ---
obs0.15996 89022 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.193 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.96→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9080 0 381 423 9884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139728
X-RAY DIFFRACTIONr_bond_other_d0.0350.0148992
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.69513234
X-RAY DIFFRACTIONr_angle_other_deg2.5051.62620718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.08551218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27622.264477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.478151428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4761563
X-RAY DIFFRACTIONr_chiral_restr0.0630.21369
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210854
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022136
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_it1.9563.3574845
X-RAY DIFFRACTIONr_mcbond_other1.9553.3574844
X-RAY DIFFRACTIONr_mcangle_it2.5365.0296054
X-RAY DIFFRACTIONr_mcangle_other2.5365.0296055
X-RAY DIFFRACTIONr_scbond_it2.5993.6934883
X-RAY DIFFRACTIONr_scbond_other2.5993.6934883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7645.447175
X-RAY DIFFRACTIONr_long_range_B_refined4.54640.6749905
X-RAY DIFFRACTIONr_long_range_B_other4.52640.5669861
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 361 -
Rwork0.162 6690 -
obs--98.68 %

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