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

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Basic information

Entry
Database: PDB / ID: 5zku
TitleCrystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 in complex with DFA-III
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
Chem-9F3 / Inulin fructotransferase (DFA-I-forming)
Similarity search - Component
Biological speciesArthrobacter chlorophenolicus A6 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.32 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 1.1Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DFA-IIIase
B: DFA-IIIase
C: DFA-IIIase
D: DFA-IIIase
E: DFA-IIIase
F: DFA-IIIase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,13312
Polymers283,1886
Non-polymers1,9466
Water5,459303
1
A: DFA-IIIase
B: DFA-IIIase
C: DFA-IIIase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5676
Polymers141,5943
Non-polymers9733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17120 Å2
ΔGint-66 kcal/mol
Surface area36690 Å2
MethodPISA
2
D: DFA-IIIase
E: DFA-IIIase
F: DFA-IIIase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5676
Polymers141,5943
Non-polymers9733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17330 Å2
ΔGint-66 kcal/mol
Surface area36680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.466, 77.175, 139.718
Angle α, β, γ (deg.)90.00, 99.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 47197.953 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter chlorophenolicus A6 (bacteria)
Gene: Achl_2895
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B8HDZ1, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-9F3 / (2R,3'S,4'S,4aR,5'R,6R,7R,7aS)-4a,5',6-tris(hydroxymethyl)spiro[3,6,7,7a-tetrahydrofuro[2,3-b][1,4]dioxine-2,2'-oxolane ]-3',4',7-triol / Beta-2,1'-alpha-2',3-Difructofuranose anhydride


Mass: 324.281 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H20O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
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 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 92637 / % possible obs: 91.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 19
Reflection shellResolution: 2.32→2.36 Å / Rmerge(I) obs: 0.361

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.32→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.141 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.691 / ESU R Free: 0.279 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24004 4830 5.1 %RANDOM
Rwork0.18818 ---
obs0.19078 90013 88.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.825 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å2-1.07 Å2
2--4.61 Å20 Å2
3----2.26 Å2
Refinement stepCycle: 1 / Resolution: 2.32→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19810 0 132 303 20245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01920387
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218041
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.93727818
X-RAY DIFFRACTIONr_angle_other_deg0.9753.00341786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41752646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06724.214954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.808152916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.11215132
X-RAY DIFFRACTIONr_chiral_restr0.0850.23152
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02123436
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024176
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_it2.4194.45310611
X-RAY DIFFRACTIONr_mcbond_other2.4174.45310604
X-RAY DIFFRACTIONr_mcangle_it3.8466.67113244
X-RAY DIFFRACTIONr_mcangle_other3.8466.67213245
X-RAY DIFFRACTIONr_scbond_it2.3784.5399776
X-RAY DIFFRACTIONr_scbond_other2.3784.5399777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7876.74314575
X-RAY DIFFRACTIONr_long_range_B_refined5.92652.07421163
X-RAY DIFFRACTIONr_long_range_B_other5.92652.07521164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.313→2.373 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 229 -
Rwork0.277 4169 -
obs--55.85 %

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