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- PDB-8beu: Structure of D188A-fructofuranosidase from Rhodotorula dairenensi... -

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Basic information

Entry
Database: PDB / ID: 8beu
TitleStructure of D188A-fructofuranosidase from Rhodotorula dairenensis in complex with raffinose
ComponentsBeta-fructofuranosidaseSucrase
KeywordsHYDROLASE / FRUCTOFURANOSIDASE / INVERTASE / HYDROLYTIC ENZYME / GLYCOSIL HYDROLASE / PREBIOTIC / OLIGOSACCHARIDE / FRUCTOOLIGOSACCHARIDE / FOS / RHODOTORULA DAIRENENSIS
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
raffinose / alpha-D-mannopyranose / DI(HYDROXYETHYL)ETHER / Beta-fructofuranosidase
Similarity search - Component
Biological speciesRhodotorula dairenensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.27 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)296,96755
Polymers282,6854
Non-polymers14,28251
Water10,016556
1
A: Beta-fructofuranosidase
B: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,54531
Polymers141,3432
Non-polymers8,20329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15300 Å2
ΔGint120 kcal/mol
Surface area38860 Å2
2
C: Beta-fructofuranosidase
D: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,42224
Polymers141,3432
Non-polymers6,08022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint85 kcal/mol
Surface area37610 Å2
Unit cell
Length a, b, c (Å)81.008, 114.544, 139.165
Angle α, β, γ (deg.)90.000, 104.580, 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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRAA142 - 671142 - 671
21SERSERTHRTHRBB142 - 671142 - 671
12SERSERTHRTHRAA142 - 671142 - 671
22SERSERTHRTHRCC142 - 671142 - 671
13CYSCYSGLNGLNAA143 - 673143 - 673
23CYSCYSGLNGLNDD143 - 673143 - 673
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 , 1 types, 4 molecules ABCD

#1: Protein
Beta-fructofuranosidase / Sucrase


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

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Sugars , 7 types, 50 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-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.: 2
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
#4: Polysaccharide
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: raffinose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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-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
#7: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 13 / 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
#8: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 27 / 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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Non-polymers , 2 types, 557 molecules

#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.92 % / Description: Bladed crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 3350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5 at 5.5 mg ml-1 concentration, 2:1 rate. Soaking: Mother liquor solution supplemented with 30 mM raffinose. 2h Cryocooling: Mother liquor ...Details: 20% PEG 3350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5 at 5.5 mg ml-1 concentration, 2:1 rate. Soaking: Mother liquor solution supplemented with 30 mM raffinose. 2h 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 19, 2021 / Details: KB Mirrors
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979264 Å / Relative weight: 1
ReflectionResolution: 2.27→46.29 Å / Num. obs: 113410 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.055 / Rrim(I) all: 0.144 / Net I/σ(I): 9.1
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 7 % / Rmerge(I) obs: 0.689 / Num. unique obs: 5618 / CC1/2: 0.866 / Rpim(I) all: 0.401 / Rrim(I) all: 0.744 / % possible all: 99.9

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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: 2.27→46.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.396 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.247 5731 5.1 %RANDOM
Rwork0.2061 ---
obs0.2082 107654 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.09 Å2 / Biso mean: 47.699 Å2 / Biso min: 21.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0.68 Å2
2--3.03 Å20 Å2
3----0.85 Å2
Refinement stepCycle: final / Resolution: 2.27→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16133 0 920 561 17614
Biso mean--75.7 45.48 -
Num. residues----2100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01317632
X-RAY DIFFRACTIONr_bond_other_d0.0050.01415139
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.71924277
X-RAY DIFFRACTIONr_angle_other_deg1.4831.63335075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80352090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99623.885798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.679152196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3981544
X-RAY DIFFRACTIONr_chiral_restr0.060.22503
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219821
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023995
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A168090.06
12B168090.06
21A168280.06
22C168280.06
31A164370.08
32D164370.08
41B169150.06
42C169150.06
51B164500.08
52D164500.08
61C164610.08
62D164610.08
LS refinement shellResolution: 2.27→2.329 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 424 -
Rwork0.268 7943 -
all-8367 -
obs--99.89 %

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