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- PDB-5zks: Crystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 -

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Basic information

Entry
Database: PDB / ID: 5zks
TitleCrystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6
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
Inulin fructotransferase (DFA-I-forming)
Similarity search - Component
Biological speciesArthrobacter chlorophenolicus A6 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)47,1981
Polymers47,1981
Non-polymers00
Water3,729207
1
A: DFA-IIIase

A: DFA-IIIase

A: DFA-IIIase


Theoretical massNumber of molelcules
Total (without water)141,5943
Polymers141,5943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area16630 Å2
ΔGint-59 kcal/mol
Surface area37230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.348, 134.348, 78.554
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

21A-705-

HOH

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Components

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


Mass: 47197.953 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 4.34 Å3/Da / Density % sol: 71.63 %
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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.525
11K, H, -L20.475
ReflectionResolution: 2→50 Å / Num. obs: 54535 / % possible obs: 99.8 % / Redundancy: 5.4 % / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2inu

2inu


Resolution: 2→38.37 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.619 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13948 2799 5.1 %RANDOM
Rwork0.10934 ---
obs0.11091 51734 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.319 Å2
Baniso -1Baniso -2Baniso -3
1-5.76 Å20 Å20 Å2
2--5.76 Å20 Å2
3----11.53 Å2
Refinement stepCycle: 1 / Resolution: 2→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 0 207 3498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193367
X-RAY DIFFRACTIONr_bond_other_d0.0010.023092
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9294594
X-RAY DIFFRACTIONr_angle_other_deg0.81737090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9845441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29324.214159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23515486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9841522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02799
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_it2.2382.7921761
X-RAY DIFFRACTIONr_mcbond_other2.2192.791760
X-RAY DIFFRACTIONr_mcangle_it2.584.1822200
X-RAY DIFFRACTIONr_mcangle_other2.584.1852201
X-RAY DIFFRACTIONr_scbond_it2.8053.0271606
X-RAY DIFFRACTIONr_scbond_other2.8053.0291607
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9734.4482394
X-RAY DIFFRACTIONr_long_range_B_refined3.14723.183738
X-RAY DIFFRACTIONr_long_range_B_other3.12222.9843666
X-RAY DIFFRACTIONr_rigid_bond_restr2.56836457
X-RAY DIFFRACTIONr_sphericity_free14.251570
X-RAY DIFFRACTIONr_sphericity_bonded5.90556526
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 227 -
Rwork0.188 3788 -
obs--99.9 %

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