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- PDB-7v1v: Difructose dianhydride I synthase/hydrolase (alphaFFase1) from Bi... -

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Basic information

Entry
Database: PDB / ID: 7v1v
TitleDifructose dianhydride I synthase/hydrolase (alphaFFase1) from Bifidobacterium dentium, ligand-free form
ComponentsDifructose dianhydride I synthase/hydrolase (alphaFFase1)
KeywordsHYDROLASE / Glycoside Hydrolase / alpha-D-fructofuranosidase / ligand-free
Function / homologyProtein of unknown function DUF2961 / Protein of unknown function (DUF2961) / metal ion binding / D(-)-TARTARIC ACID / DUF2961 domain-containing protein
Function and homology information
Biological speciesBifidobacterium dentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 1.1Feb 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 1.2Nov 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)319,04716
Polymers318,2706
Non-polymers77710
Water43,6502423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51860 Å2
ΔGint-359 kcal/mol
Surface area80370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.552, 156.970, 100.909
Angle α, β, γ (deg.)90.000, 109.930, 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2423 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M di-sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→49.69 Å / Num. obs: 206183 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 8.99 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.061 / Rrim(I) all: 0.116 / Net I/σ(I): 10.3
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 10181 / CC1/2: 0.8 / Rpim(I) all: 0.283 / Rrim(I) all: 0.518 / % possible all: 99.9

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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: 1.96→49.69 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.421 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 10456 5.1 %RANDOM
Rwork0.1526 ---
obs0.1546 195690 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.27 Å2 / Biso mean: 18.101 Å2 / Biso min: 5.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å20.68 Å2
2---1.4 Å2-0 Å2
3---0.54 Å2
Refinement stepCycle: final / Resolution: 1.96→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21732 0 42 2423 24197
Biso mean--39.96 25.3 -
Num. residues----2678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01322460
X-RAY DIFFRACTIONr_bond_other_d0.0020.01720034
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.64930584
X-RAY DIFFRACTIONr_angle_other_deg1.3961.57946284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.78852672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51122.9411292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.509153496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.80415120
X-RAY DIFFRACTIONr_chiral_restr0.0820.22786
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0225784
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025456
LS refinement shellResolution: 1.96→2.01 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.248 774 -
Rwork0.199 14485 -
obs--99.89 %

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