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

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Basic information

Entry
Database: PDB / ID: 5zky
TitleCrystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 without its lid
ComponentsDFA-IIIase
KeywordsHYDROLASE / hydrolyze difructose anhydride / parallel beta helix / endoenzyme / Lyase
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
Inulin fructotransferase (DFA-I-forming)
Similarity search - Component
Biological speciesArthrobacter chlorophenolicus A6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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


Theoretical massNumber of molelcules
Total (without water)44,8261
Polymers44,8261
Non-polymers00
Water3,009167
1
A: DFA-IIIase

A: DFA-IIIase

A: DFA-IIIase


Theoretical massNumber of molelcules
Total (without water)134,4793
Polymers134,4793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area14270 Å2
ΔGint-51 kcal/mol
Surface area35450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.463, 187.463, 187.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 79.91 %
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: 2.1→50 Å / Num. obs: 63519 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 12.4
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.839 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16482 3287 5.2 %RANDOM
Rwork0.14532 ---
obs0.14633 60206 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.292 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 0 167 3282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193188
X-RAY DIFFRACTIONr_bond_other_d0.0020.022814
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9234345
X-RAY DIFFRACTIONr_angle_other_deg0.97836514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2165411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67324.026154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51715459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5191522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
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_it2.4033.2761650
X-RAY DIFFRACTIONr_mcbond_other2.3963.2741649
X-RAY DIFFRACTIONr_mcangle_it2.9084.912059
X-RAY DIFFRACTIONr_mcangle_other2.9074.9132060
X-RAY DIFFRACTIONr_scbond_it2.6873.4741538
X-RAY DIFFRACTIONr_scbond_other2.6873.4761539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2775.1432287
X-RAY DIFFRACTIONr_long_range_B_refined3.67439.2133383
X-RAY DIFFRACTIONr_long_range_B_other3.60639.1063361
X-RAY DIFFRACTIONr_rigid_bond_restr1.93736001
X-RAY DIFFRACTIONr_sphericity_free22.319596
X-RAY DIFFRACTIONr_sphericity_bonded7.81956009
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 280 -
Rwork0.211 4365 -
obs--99.91 %

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