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- PDB-3u14: Structure of D50A-fructofuranosidase from Schwanniomyces occident... -

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Basic information

Entry
Database: PDB / ID: 3u14
TitleStructure of D50A-fructofuranosidase from Schwanniomyces occidentalis complexed with inulin
ComponentsFructofuranosidase
KeywordsHYDROLASE / Glycosidase GH32 / Beta-Propeller / Carbohydrate/Sugar Binding / Glycosylations
Function / homology
Function and homology information


beta-fructofuranosidase / sucrose alpha-glucosidase activity / sucrose catabolic process / fungal-type vacuole / 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 / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase domain; family 43 ...Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSchwanniomyces occidentalis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacement, FOURIER SYNTHESIS / Resolution: 2.24 Å
AuthorsSainz-Polo, M.A. / Sanz-Aparicio, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and kinetic insights reveal that the amino acid pair GLN228/ASN254 modulates the transfructosylating specificity of Schwanniomyces occidentalis beta-fructofuranosidase, an enzyme ...Title: Structural and kinetic insights reveal that the amino acid pair GLN228/ASN254 modulates the transfructosylating specificity of Schwanniomyces occidentalis beta-fructofuranosidase, an enzyme that produces prebiotics.
Authors: Sainz-Polo, M.A. / Gonzalez-Perez, D. / Gonzalez, B. / Plou, F.J. / Fernandez-Lobato, M. / Sanz-Aparicio, J.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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)125,92912
Polymers122,1782
Non-polymers3,75110
Water11,115617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.980, 107.670, 96.460
Angle α, β, γ (deg.)90.00, 91.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 27 - 535 / Label seq-ID: 27 - 535

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

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Components

#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: Escherichia coli (E. coli) / References: UniProt: E5D0X5*PLUS, beta-fructofuranosidase
#2: 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)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DFrufb2-1DFrufb2-1DFrufb2-1DFrufb2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[ha122h-2b_2-5]/1-1-1-1-1-1/a1-b2_b1-c2_c1-d2_d1-e2_e1-f2WURCSPDB2Glycan 1.1.0
[][<C6O4>]{[(1+2)][b-D-Fruf]{}}LINUCSPDB-CARE
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsINULIN IS COMPOSED OF FRU 1000-1005
Sequence detailsTHE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN, UNIPROT P24133 HAS BEEN SUPERSEEDED BY CQ890277 ...THE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN, UNIPROT P24133 HAS BEEN SUPERSEEDED BY CQ890277 ON THE GENBANK, WHICH CONTAINS THE UPDATED SEQUENCE. IN ADDITION, THIS ENTRY CONTAINS THE MUTATION D50A

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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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 8
Details: 15% PEG 6000, 3% MPD, 0.2M MgCl2, 0.1M HCl-Tris pH 8, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.24→107.67 Å / Num. all: 65603 / Num. obs: 65603 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.14 / Rsym value: 0.14
Reflection shellResolution: 2.24→2.36 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / Num. unique all: 9367 / Rsym value: 0.5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CCP4phasing
RefinementMethod to determine structure: Molecular Replacement, FOURIER SYNTHESIS
Starting model: 3KF3

3kf3


Resolution: 2.24→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.821 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23146 3265 5.1 %RANDOM
Rwork0.19369 ---
all0.1956 61336 --
obs0.1956 61336 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0.63 Å2
2--0.49 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.24→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8262 0 244 617 9123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228773
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.95911970
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64651016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88525.268448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.127151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8391522
X-RAY DIFFRACTIONr_chiral_restr0.0970.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216770
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6271.55080
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23228272
X-RAY DIFFRACTIONr_scbond_it1.75533693
X-RAY DIFFRACTIONr_scangle_it2.9254.53692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2036tight positional0.050.05
2095medium positional0.050.5
2036tight thermal0.10.5
2095medium thermal0.112
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 256 -
Rwork0.252 4510 -
obs--97.82 %

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