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- PDB-1y9g: Crystal structure of exo-inulinase from Aspergillus awamori compl... -

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Basic information

Entry
Database: PDB / ID: 1y9g
TitleCrystal structure of exo-inulinase from Aspergillus awamori complexed with fructose
Componentsexo-inulinase
KeywordsHYDROLASE / Exo-inulinase / Aspergillus awamori / Glycoside hydrolase family 32 / Crystallographic structure / Complex with fructose
Function / homology
Function and homology information


fructan beta-fructosidase / fructan beta-fructosidase activity / polysaccharide catabolic process / extracellular region
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
beta-D-fructofuranose / : / Extracellular exo-inulinase inuE
Similarity search - Component
Biological speciesAspergillus awamori (mold)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.87 Å
AuthorsNagem, R.A.P. / Rojas, A.L. / Golubev, A.M. / Korneeva, O.S. / Eneyskaya, E.V. / Kulminskaya, A.A. / Neustroev, K.N. / Polikarpov, I.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of exo-inulinase from Aspergillus awamori: the enzyme fold and structural determinants of substrate recognition
Authors: Nagem, R.A.P. / Rojas, A.L. / Golubev, A.M. / Korneeva, O.S. / Eneyskaya, E.V. / Kulminskaya, A.A. / Neustroev, K.N. / Polikarpov, I.
#1: Journal: BIOCHEM.J. / Year: 2002
Title: Purification, characterization, gene cloning and preliminary X-ray data of the exo-inulinase from Aspergillus awamori
Authors: Arand, M. / Golubev, A.M. / Neto, J.R. / Polikarpov, I. / Wattiez, R. / Korneeva, O.S. / Eneyskaya, E.V. / Kulminskaya, A.A. / Shabalin, K.A. / Shishliannikov, S.M. / Chepurnaya, O.V. / Neustroev, K.N.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 20, 2017Group: Database references / Category: pdbx_database_related
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_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: exo-inulinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4576
Polymers57,1891
Non-polymers1,2685
Water13,601755
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.904, 94.371, 67.617
Angle α, β, γ (deg.)90.00, 107.10, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer generated from the structure in the asymmetric unit by the identity operation.

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Components

#1: Protein exo-inulinase


Mass: 57188.633 Da / Num. of mol.: 1 / Fragment: sequence database residues 20-537 / Source method: isolated from a natural source / Source: (natural) Aspergillus awamori (mold) / Strain: 2250
References: GenBank: 14787237, UniProt: Q96TU3*PLUS, fructan beta-fructosidase
#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.: 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)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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: Sugar ChemComp-FRU / beta-D-fructofuranose / Fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15% PEG3350, 1 mM sodium cacodylate, 20-100 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2003
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.87→24.05 Å / Num. all: 49450 / Num. obs: 41994 / % possible obs: 84.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.1
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.2 / % possible all: 75.58

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.87→24.05 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.072 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.146 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19473 2113 5 %RANDOM
Rwork0.14869 ---
obs0.151 41994 84.9 %-
all-49450 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20.18 Å2
2--1.1 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.87→24.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 82 755 4879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0214260
X-RAY DIFFRACTIONr_bond_other_d0.0020.023548
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.9355829
X-RAY DIFFRACTIONr_angle_other_deg0.92538264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6185516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04224.541196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55415594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1311512
X-RAY DIFFRACTIONr_chiral_restr0.1320.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
X-RAY DIFFRACTIONr_nbd_refined0.1910.2823
X-RAY DIFFRACTIONr_nbd_other0.2650.24431
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22084
X-RAY DIFFRACTIONr_nbtor_other0.090.22349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2562
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.229
X-RAY DIFFRACTIONr_mcbond_it1.281.53220
X-RAY DIFFRACTIONr_mcbond_other0.3511.51051
X-RAY DIFFRACTIONr_mcangle_it1.55424149
X-RAY DIFFRACTIONr_scbond_it2.71332057
X-RAY DIFFRACTIONr_scangle_it3.664.51680
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 121 -
Rwork0.264 2630 -
obs-2630 75.58 %

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