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- PDB-8hui: Crystal structure of DFA I-forming Inulin Lyase from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 8hui
TitleCrystal structure of DFA I-forming Inulin Lyase from Streptomyces peucetius subsp. caesius ATCC 27952 in complex with GF4, DFA I, and fructose
ComponentsFructotransferase
KeywordsLYASE / right-handed beta-helix protein / DFA I-forming inulin lyase / complex
Function / homology
Function and homology information


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
Similarity search - Domain/homology
beta-D-fructofuranose / DI(HYDROXYETHYL)ETHER / Fructotransferase
Similarity search - Component
Biological speciesStreptomyces peucetius subsp. caesius ATCC 27952 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsCheng, M. / Rao, Y.J. / Mu, W.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31922073 China
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Structural Insights into the Catalytic Cycle of Inulin Fructotransferase: From Substrate Anchoring to Product Releasing.
Authors: Cheng, M. / Hou, X. / Huang, Z. / Chen, Z. / Ni, D. / Zhang, W. / Rao, Y. / Mu, W.
History
DepositionDec 24, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructotransferase
B: Fructotransferase
C: Fructotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,80113
Polymers128,2583
Non-polymers4,54310
Water16,988943
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22290 Å2
ΔGint67 kcal/mol
Surface area31230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.760, 105.600, 131.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Fructotransferase / inulin lyase [DFA I-forming]


Mass: 42752.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius subsp. caesius ATCC 27952 (bacteria)
Gene: CGZ69_03210 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2D3U3Z1, inulin fructotransferase (DFA-I-forming)

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Sugars , 3 types, 7 molecules

#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-fructofuranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DFrufb2-1DFrufaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,2/[ha122h-2a_2-5]/1-1/a1-b2_a2-b1WURCSPDB2Glycan 1.1.0
#3: Polysaccharide
beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D- ...beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 4 / Source method: isolated from a natural source
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DFrufb2-1DFrufb2-1DGlcpaGlycam 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
#4: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 946 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 943 / 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: 2.66 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES monohydrate, 12% Polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.44→45.84 Å / Num. obs: 247198 / % possible obs: 99.7 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.105 / Net I/σ(I): 17.6
Reflection shellResolution: 1.44→1.49 Å / Rmerge(I) obs: 0.921 / Num. unique obs: 24175 / CC1/2: 0.837 / Rrim(I) all: 0.962

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Processing

Software
NameVersionClassification
XSCALEBUILT=20220220data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSBUILT=20220220data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→45.84 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1681 1991 -
Rwork0.1539 --
obs0.154 247095 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8892 0 303 943 10138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089589
X-RAY DIFFRACTIONf_angle_d1.1913171
X-RAY DIFFRACTIONf_dihedral_angle_d9.9081321
X-RAY DIFFRACTIONf_chiral_restr0.0861586
X-RAY DIFFRACTIONf_plane_restr0.0071675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.470.36631440.30817011X-RAY DIFFRACTION98
1.47-1.510.2451410.233717433X-RAY DIFFRACTION100
1.51-1.560.24841450.223517348X-RAY DIFFRACTION100
1.56-1.610.18421370.183517467X-RAY DIFFRACTION100
1.61-1.660.20331430.168317384X-RAY DIFFRACTION100
1.66-1.730.20221480.150517463X-RAY DIFFRACTION100
1.73-1.810.18541340.143117447X-RAY DIFFRACTION100
1.81-1.90.14581450.145617469X-RAY DIFFRACTION100
1.9-2.020.20181430.161417500X-RAY DIFFRACTION100
2.02-2.180.14531360.14717480X-RAY DIFFRACTION100
2.18-2.40.16141430.149717516X-RAY DIFFRACTION99
2.4-2.750.14021470.134517606X-RAY DIFFRACTION100
2.75-3.460.15451410.137117751X-RAY DIFFRACTION100
3.46-45.840.13161440.135618229X-RAY DIFFRACTION100

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