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- PDB-5zl5: Crystal structure of DFA-IIIase mutant C387A from Arthrobacter ch... -

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Basic information

Entry
Database: PDB / ID: 5zl5
TitleCrystal structure of DFA-IIIase mutant C387A from Arthrobacter chlorophenolicus A6
ComponentsDFA-IIIase C387A mutant
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 / SYNCHROTRON / Resolution: 1.65 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

Downloads & links

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Assembly

Deposited unit
A: DFA-IIIase C387A mutant
B: DFA-IIIase C387A mutant
C: DFA-IIIase C387A mutant
D: DFA-IIIase C387A mutant
E: DFA-IIIase C387A mutant
F: DFA-IIIase C387A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,45611
Polymers282,9956
Non-polymers4605
Water38,7322150
1
A: DFA-IIIase C387A mutant
B: DFA-IIIase C387A mutant
D: DFA-IIIase C387A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,6825
Polymers141,4983
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17450 Å2
ΔGint-76 kcal/mol
Surface area36650 Å2
MethodPISA
2
C: DFA-IIIase C387A mutant
E: DFA-IIIase C387A mutant
F: DFA-IIIase C387A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,7746
Polymers141,4983
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17580 Å2
ΔGint-72 kcal/mol
Surface area36720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.296, 79.530, 140.974
Angle α, β, γ (deg.)90.00, 100.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DFA-IIIase C387A mutant / difructose anhydride hydrolase / Inulin fructotransferase (DFA-I-forming)


Mass: 47165.891 Da / Num. of mol.: 6 / Mutation: C387A
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2150 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
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: 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: 1.65→50 Å / Num. obs: 290222 / % possible obs: 96.2 % / Redundancy: 5.8 % / Net I/σ(I): 14.7
Reflection shellResolution: 1.65→1.68 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.658 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17295 14338 4.9 %RANDOM
Rwork0.13156 ---
obs0.13359 275848 95.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.667 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.5 Å2
2--0.77 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19659 0 30 2150 21839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01920121
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218511
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.92827419
X-RAY DIFFRACTIONr_angle_other_deg0.965342430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18452614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41224.185951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.791152906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.26815132
X-RAY DIFFRACTIONr_chiral_restr0.1010.23099
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02123609
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024771
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_it1.3241.38810480
X-RAY DIFFRACTIONr_mcbond_other1.3241.38710479
X-RAY DIFFRACTIONr_mcangle_it1.6982.07913080
X-RAY DIFFRACTIONr_mcangle_other1.6972.07913081
X-RAY DIFFRACTIONr_scbond_it1.6441.5949641
X-RAY DIFFRACTIONr_scbond_other1.6441.5949641
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9792.31314338
X-RAY DIFFRACTIONr_long_range_B_refined3.06912.63623589
X-RAY DIFFRACTIONr_long_range_B_other3.06912.63723590
X-RAY DIFFRACTIONr_rigid_bond_restr1.608338632
X-RAY DIFFRACTIONr_sphericity_free26.145552
X-RAY DIFFRACTIONr_sphericity_bonded6.198539812
LS refinement shellResolution: 1.652→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 1057 -
Rwork0.187 20521 -
obs--96.9 %

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