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- PDB-7v1w: Difructose dianhydride I synthase/hydrolase (alphaFFase1) from Bi... -

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Basic information

Entry
Database: PDB / ID: 7v1w
TitleDifructose dianhydride I synthase/hydrolase (alphaFFase1) from Bifidobacterium dentium in complex with beta-D-arabinofuranose
ComponentsDifructose dianhydride I synthase/hydrolase (alphaFFase1)
KeywordsHYDROLASE / Glycoside Hydrolase / alpha-D-fructofuranosidase / beta-D-arabinofuranose complex
Function / homologyProtein of unknown function DUF2961 / Protein of unknown function (DUF2961) / metal ion binding / beta-D-arabinofuranose / DUF2961 domain-containing protein
Function and homology information
Biological speciesBifidobacterium dentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKashima, T. / Arakawa, T. / Yamada, C. / Fujita, K. / Fushinobu, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)26660083 Japan
Japan Society for the Promotion of Science (JSPS)24380053 Japan
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family.
Authors: Kashima, T. / Okumura, K. / Ishiwata, A. / Kaieda, M. / Terada, T. / Arakawa, T. / Yamada, C. / Shimizu, K. / Tanaka, K. / Kitaoka, M. / Ito, Y. / Fujita, K. / Fushinobu, S.
History
DepositionAug 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 2.0Jan 12, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_conf / struct_conn / struct_mon_prot_cis
Item: _entity.pdbx_number_of_molecules / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._entity.pdbx_number_of_molecules / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.percent_reflns_obs / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.pdbx_omega_angle
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Difructose dianhydride I synthase/hydrolase (alphaFFase1)
B: Difructose dianhydride I synthase/hydrolase (alphaFFase1)
C: Difructose dianhydride I synthase/hydrolase (alphaFFase1)
D: Difructose dianhydride I synthase/hydrolase (alphaFFase1)
E: Difructose dianhydride I synthase/hydrolase (alphaFFase1)
F: Difructose dianhydride I synthase/hydrolase (alphaFFase1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,41118
Polymers318,2706
Non-polymers1,14112
Water31,4901748
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50960 Å2
ΔGint-342 kcal/mol
Surface area79940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.451, 156.707, 100.849
Angle α, β, γ (deg.)90.000, 110.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Difructose dianhydride I synthase/hydrolase (alphaFFase1)


Mass: 53045.027 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium dentium (bacteria) / Gene: BDLFYP24_02130 / Plasmid: pET23d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6L9SN29
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-BXX / beta-D-arabinofuranose / beta-D-arabinose / D-arabinose / arabinose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DArafbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-arabinofuranoseCOMMON NAMEGMML 1.0
b-D-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1748 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M di-sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2019
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→48.77 Å / Num. obs: 237104 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.05 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.05 / Rrim(I) all: 0.132 / Net I/σ(I): 10.9
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 11654 / CC1/2: 0.811 / Rpim(I) all: 0.489 / Rrim(I) all: 0.912 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KQ7

4kq7


Resolution: 1.86→48.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.587 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 12087 5.1 %RANDOM
Rwork0.1683 ---
obs0.1701 224977 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.33 Å2 / Biso mean: 27.033 Å2 / Biso min: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20.02 Å2
2---0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.86→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21768 0 66 1748 23582
Biso mean--26.19 31.67 -
Num. residues----2682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01322566
X-RAY DIFFRACTIONr_bond_other_d0.0010.01520070
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.65230672
X-RAY DIFFRACTIONr_angle_other_deg1.3641.58246386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83252676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91722.9631296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.711153504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.19715120
X-RAY DIFFRACTIONr_chiral_restr0.0810.22808
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0225812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025460
LS refinement shellResolution: 1.865→1.913 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 878 -
Rwork0.283 16552 -
all-17430 -
obs--99.77 %

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