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

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Basic information

Entry
Database: PDB / ID: 5zkw
TitleCrystal structure of DFA-IIIase from Arthrobacter chlorophenolicus A6 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
Inulin fructotransferase (DFA-I-forming)
Similarity search - Component
Biological speciesArthrobacter chlorophenolicus A6 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.86 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 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 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)285,20510
Polymers283,1886
Non-polymers2,0184
Water24,0501335
1
A: DFA-IIIase
B: DFA-IIIase
D: DFA-IIIase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,6035
Polymers141,5943
Non-polymers1,0092
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18040 Å2
ΔGint-35 kcal/mol
Surface area35680 Å2
MethodPISA
2
C: DFA-IIIase
E: DFA-IIIase
F: DFA-IIIase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,6035
Polymers141,5943
Non-polymers1,0092
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17910 Å2
ΔGint-35 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.121, 79.233, 140.571
Angle α, β, γ (deg.)90.00, 100.38, 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: Polysaccharide
alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose-(2-1)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-2DFrufb2-1DFrufbGlycam 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.: 1335 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350,0.1 M Sodium malonate (pH 4.2)

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Data collection

DiffractionMean temperature: 100 K
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: 1.86→50 Å / Num. obs: 209495 / % possible obs: 99.2 % / Redundancy: 5.4 % / Net I/σ(I): 20.8
Reflection shellResolution: 1.86→1.89 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.794 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 10583 5.1 %RANDOM
Rwork0.16631 ---
obs0.16773 198888 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.728 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0.86 Å2
2--0.8 Å20 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19120 0 136 1335 20591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01919684
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217450
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.93626843
X-RAY DIFFRACTIONr_angle_other_deg0.932340412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16152528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16724.114926
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.433152830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.22115130
X-RAY DIFFRACTIONr_chiral_restr0.080.23051
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02122487
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024035
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_it1.3322.74410163
X-RAY DIFFRACTIONr_mcbond_other1.3322.74410162
X-RAY DIFFRACTIONr_mcangle_it2.1854.10112674
X-RAY DIFFRACTIONr_mcangle_other2.1844.10212675
X-RAY DIFFRACTIONr_scbond_it1.4432.8979521
X-RAY DIFFRACTIONr_scbond_other1.4432.8979521
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3874.29714170
X-RAY DIFFRACTIONr_long_range_B_refined4.22533.08321013
X-RAY DIFFRACTIONr_long_range_B_other4.13132.82420717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.858→1.906 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 706 -
Rwork0.241 13327 -
obs--90.08 %

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