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- PDB-5zl4: Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicu... -

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Basic information

Entry
Database: PDB / ID: 5zl4
TitleCrystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 wihout its lid in complex with GF2
ComponentsDFA-IIIase
KeywordsHYDROLASE / hydrolyze difructose anhydride / parallel beta helix / endoenzyme
Function / homology
Function and homology information


inulin fructotransferase (DFA-I-forming) / inulin fructotransferase (DFA-I-forming) activity / transferase activity
Similarity search - Function
Periplasmic copper-binding protein NosD, beta helix domain / Periplasmic copper-binding protein (NosD) / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
1-kestose / Inulin fructotransferase (DFA-I-forming)
Similarity search - Component
Biological speciesArthrobacter chlorophenolicus A6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsYu, S.H. / Shen, H. / Li, X. / Mu, W.M.
CitationJournal: Acs Catalysis / Year: 2018
Title: Structural and functional basis of difructose anhydride III hydrolase, which sequentially converts inulin using the same catalytic residue
Authors: Yu, S.H. / Shen, H. / Cheng, Y.Y. / Zhu, Y.Y. / Li, X. / Mu, W.M.
History
DepositionMar 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DFA-IIIase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3312
Polymers44,8261
Non-polymers5041
Water52229
1
A: DFA-IIIase
hetero molecules

A: DFA-IIIase
hetero molecules

A: DFA-IIIase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9926
Polymers134,4793
Non-polymers1,5133
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16770 Å2
ΔGint-68 kcal/mol
Surface area35490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.407, 187.407, 187.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

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Components

#1: Protein DFA-IIIase / difructose anhydride hydrolase / Inulin fructotransferase (DFA-I-forming)


Mass: 44826.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DFA-IIIase wihout its lid, Residues 376-407 were deleted and replaced with linker residues SNVDTQH.
Source: (gene. exp.) Arthrobacter chlorophenolicus A6 (bacteria)
Gene: Achl_2895
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B8HDZ1, inulin fructotransferase (DFA-III-forming)
#2: Polysaccharide beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / 1-kestose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: 1-kestose
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-2/a1-b2_b1-c2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 6.12 Å3/Da / Density % sol: 79.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350, 0.1M Sodium malonate (pH 4.2)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 22038 / % possible obs: 99.9 % / Redundancy: 7.8 % / Net I/σ(I): 18.6
Reflection shellResolution: 3→3.05 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 3→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 20.62 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1788 1131 5.1 %RANDOM
Rwork0.14734 ---
obs0.14894 20875 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.822 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 34 29 3191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193238
X-RAY DIFFRACTIONr_bond_other_d0.0030.022955
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9384420
X-RAY DIFFRACTIONr_angle_other_deg0.993.0056779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.52524.026154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92215459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2641522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02775
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_it3.7485.6161663
X-RAY DIFFRACTIONr_mcbond_other3.725.6151662
X-RAY DIFFRACTIONr_mcangle_it5.1748.4172077
X-RAY DIFFRACTIONr_mcangle_other5.1758.4182078
X-RAY DIFFRACTIONr_scbond_it3.8325.8451574
X-RAY DIFFRACTIONr_scbond_other3.8395.8461575
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9518.72344
X-RAY DIFFRACTIONr_long_range_B_refined5.98865.443252
X-RAY DIFFRACTIONr_long_range_B_other5.98765.4513253
X-RAY DIFFRACTIONr_rigid_bond_restr0.78836189
X-RAY DIFFRACTIONr_sphericity_free27.302514
X-RAY DIFFRACTIONr_sphericity_bonded10.88156133
LS refinement shellResolution: 2.999→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 92 -
Rwork0.235 1516 -
obs--99.2 %

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