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- PDB-8bet: Structure of D188A-fructofuranosidase from Rhodotorula dairenesis... -

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Basic information

Entry
Database: PDB / ID: 8bet
TitleStructure of D188A-fructofuranosidase from Rhodotorula dairenesis in complex with sucrose
ComponentsBeta-fructofuranosidase
KeywordsHYDROLASE / FRUCTOFURANOSIDASE / INVERTASE / HYDROLYTIC ENZYME / GLYCOSIL HYDROLASE / PREBIOTIC / OLIGOSACCHARIDE / FRUCTOOLIGOSACCHARIDE / FOS / RHODOTORULA DAIRENENSIS / COMPLEXES
Function / homology
Function and homology information


beta-fructofuranosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
sucrose / alpha-D-mannopyranose / Beta-fructofuranosidase
Similarity search - Component
Biological speciesRhodotorula dairenensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.38 Å
AuthorsJimenez-Ortega, E. / Sanz-Aparicio, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: Int J Mol Sci / Year: 2022
Title: Insights into the Structure of the Highly Glycosylated Ffase from Rhodotorula dairenensis Enhance Its Biotechnological Potential.
Authors: Jimenez-Ortega, E. / Narmontaite, E. / Gonzalez-Perez, B. / Plou, F.J. / Fernandez-Lobato, M. / Sanz-Aparicio, J.
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: Beta-fructofuranosidase
B: Beta-fructofuranosidase
C: Beta-fructofuranosidase
D: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,43455
Polymers282,6854
Non-polymers13,74951
Water12,502694
1
A: Beta-fructofuranosidase
B: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,39627
Polymers141,3432
Non-polymers6,05425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint84 kcal/mol
Surface area37070 Å2
2
C: Beta-fructofuranosidase
D: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,03828
Polymers141,3432
Non-polymers7,69526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint110 kcal/mol
Surface area37940 Å2
Unit cell
Length a, b, c (Å)80.343, 112.813, 139.083
Angle α, β, γ (deg.)90.000, 104.740, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTRPTRPAA142 - 672142 - 672
21SERSERTRPTRPBB142 - 672142 - 672
12SERSERTRPTRPAA142 - 672142 - 672
22SERSERTRPTRPCC142 - 672142 - 672
13CYSCYSTHRTHRAA143 - 671143 - 671
23CYSCYSTHRTHRDD143 - 671143 - 671
14SERSERTRPTRPBB142 - 672142 - 672
24SERSERTRPTRPCC142 - 672142 - 672
15CYSCYSTRPTRPBB143 - 672143 - 672
25CYSCYSTRPTRPDD143 - 672143 - 672
16CYSCYSTRPTRPCC143 - 672143 - 672
26CYSCYSTRPTRPDD143 - 672143 - 672

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Non-polymers , 2 types, 698 molecules ABCD

#1: Protein
Beta-fructofuranosidase


Mass: 70671.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodotorula dairenensis (fungus) / Gene: INV / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115 / References: UniProt: A0A856TAI5, beta-fructofuranosidase
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 6 types, 51 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.54 % / Description: Bladed crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% PEG 3350, 0.2 M MgCl2, 0.1 M BIS-TRIS pH 5.5 at 5.1 mg mL-1 concentration, 1:1 rate. Soaking: Mother liquor solution supplemented with 30 mM sucrose. 1h 15 min. Cryocooling: Mother ...Details: 18% PEG 3350, 0.2 M MgCl2, 0.1 M BIS-TRIS pH 5.5 at 5.1 mg mL-1 concentration, 1:1 rate. Soaking: Mother liquor solution supplemented with 30 mM sucrose. 1h 15 min. Cryocooling: Mother liquor solution supplemented with 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979264 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2021 / Details: KB Mirrors
RadiationMonochromator: Si(111) channel-cut, cryocoole / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979264 Å / Relative weight: 1
ReflectionResolution: 2.38→45.69 Å / Num. obs: 96053 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Net I/σ(I): 11.8
Reflection shellResolution: 2.38→2.42 Å / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4777 / CC1/2: 0.876 / Rpim(I) all: 0.272 / Rrim(I) all: 0.731

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSVersion February 5, 2021data reduction
XDSVersion February 5, 2021data scaling
REFMAC5.8.0267phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 8BEQ

8beq


Resolution: 2.38→45.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.684 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 4728 4.9 %RANDOM
Rwork0.1843 ---
obs0.1861 91288 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.59 Å2 / Biso mean: 37.081 Å2 / Biso min: 17.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å2-0.79 Å2
2--1.15 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 2.38→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16146 0 883 694 17723
Biso mean--64.57 36.83 -
Num. residues----2103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01317610
X-RAY DIFFRACTIONr_bond_other_d0.0060.01715111
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.71724262
X-RAY DIFFRACTIONr_angle_other_deg1.3881.63135016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56152095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17423.869796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.531152195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2971544
X-RAY DIFFRACTIONr_chiral_restr0.060.22495
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219852
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023997
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A170690.07
12B170690.07
21A171580.06
22C171580.06
31A170590.06
32D170590.06
41B171100.07
42C171100.07
51B170560.07
52D170560.07
61C171460.06
62D171460.06
LS refinement shellResolution: 2.38→2.442 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 352 -
Rwork0.24 6743 -
all-7095 -
obs--99.78 %

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