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- PDB-6s2b: Structure of beta-fructofuranosidase from Schwanniomyces occident... -

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Basic information

Entry
Database: PDB / ID: 6s2b
TitleStructure of beta-fructofuranosidase from Schwanniomyces occidentalis complexed with fructosyl-erythritol
ComponentsFructofuranosidase
KeywordsHYDROLASE / BETA-FRUCTOFURANOSIDASE / GLYCOSIDASE / CARBOHYDRATE / CARBOHYDRATE METABOLISM / POLISACCHARIDE DEGRADATION / COMPLEX / FRUCTOSYL-ERYTHRITOL / FRUCTOSYLATION / TRANSFRUCTOSYLATION / FRUCTOOLIGOSACCHARIDES / FRUCTO-CONJUGATES
Function / homology
Function and homology information


beta-fructofuranosidase / sucrose catabolic process / sucrose alpha-glucosidase activity / fungal-type vacuole / extracellular region / metal ion binding
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
Chem-KTE / Fructofuranosidase
Similarity search - Component
Biological speciesSchwanniomyces occidentalis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsJimenez-Ortega, E. / Sanz-Aparicio, J.
CitationJournal: Sci Rep / Year: 2021
Title: New insights into the molecular mechanism behind mannitol and erythritol fructosylation by beta-fructofuranosidase from Schwanniomyces occidentalis.
Authors: Rodrigo-Frutos, D. / Jimenez-Ortega, E. / Piedrabuena, D. / Ramirez-Escudero, M. / Miguez, N. / Plou, F.J. / Sanz-Aparicio, J. / Fernandez-Lobato, M.
History
DepositionJun 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 13, 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: Fructofuranosidase
B: Fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,71617
Polymers122,1782
Non-polymers3,53915
Water15,277848
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint3 kcal/mol
Surface area36840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.483, 92.540, 116.108
Angle α, β, γ (deg.)90.00, 104.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 24 - 535 / Label seq-ID: 24 - 535

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fructofuranosidase


Mass: 61088.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schwanniomyces occidentalis (fungus) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): Y02321 / References: UniProt: E5D0X5, beta-fructofuranosidase

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Sugars , 3 types, 10 molecules

#2: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 8
Source method: isolated from a genetically manipulated source
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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Non-polymers , 4 types, 853 molecules

#5: Chemical ChemComp-KTE / (2~{S},3~{R})-4-[(2~{R},3~{S},4~{S},5~{R})-2,5-bis(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxybutane-1,2,3-triol


Mass: 284.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O9 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.41 % / Description: Thick plates
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 6000, 0.2 M MgCl2, and 0.1 M HEPES pH 7.0, by mixing 1 uL of protein with 0.5 uL of mother liquor. Crystals were transferred to a soaking solution containing mother liquor and 66 mM ...Details: 20% PEG 6000, 0.2 M MgCl2, and 0.1 M HEPES pH 7.0, by mixing 1 uL of protein with 0.5 uL of mother liquor. Crystals were transferred to a soaking solution containing mother liquor and 66 mM fructosyl-erythritol for 4 hours, and subsequently to a fresh drop supplemented with 25% ethylene glycol .

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2016 / Details: KB focusing mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.88→49.33 Å / Num. obs: 98961 / % possible obs: 98.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 17.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.059 / Rrim(I) all: 0.137 / Net I/σ(I): 9.2
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3 / Num. unique obs: 4791 / CC1/2: 0.773 / Rpim(I) all: 0.3 / Rrim(I) all: 0.7 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless7.0.016data scaling
MOLREP7.0.016phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KF3

3kf3


Resolution: 1.88→49.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.708 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17853 4859 4.9 %RANDOM
Rwork0.15391 ---
obs0.15512 94088 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.584 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-0.36 Å2
2---0.09 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.88→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8308 0 226 849 9383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138824
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177606
X-RAY DIFFRACTIONr_angle_refined_deg1.451.67512047
X-RAY DIFFRACTIONr_angle_other_deg1.3191.60617791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.17751032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72224.622476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.585151359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9691522
X-RAY DIFFRACTIONr_chiral_restr0.0720.21168
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021854
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_it1.3031.7724113
X-RAY DIFFRACTIONr_mcbond_other1.3031.7714112
X-RAY DIFFRACTIONr_mcangle_it2.0612.655144
X-RAY DIFFRACTIONr_mcangle_other2.062.655145
X-RAY DIFFRACTIONr_scbond_it2.0372.0744711
X-RAY DIFFRACTIONr_scbond_other2.0362.0744712
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.33.0276902
X-RAY DIFFRACTIONr_long_range_B_refined4.83621.6439657
X-RAY DIFFRACTIONr_long_range_B_other4.83521.6439658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17962 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 375 -
Rwork0.216 6845 -
obs--97.74 %

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