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- PDB-7fdz: Levansucrase from Brenneria sp. EniD 312 with sucrose -

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Basic information

Entry
Database: PDB / ID: 7fdz
TitleLevansucrase from Brenneria sp. EniD 312 with sucrose
ComponentsLevansucrase
KeywordsTRANSFERASE / Levansucrase / fructosyltransferase / levan synthesis
Function / homology
Function and homology information


levansucrase / levansucrase activity / carbohydrate utilization / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 68 / Levansucrase/Invertase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
sucrose / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / levansucrase
Similarity search - Component
Biological speciesBrenneria sp. EniD312 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsXu, W. / Hou, X.D. / Rao, Y.J. / Pijning, T. / Guskov, A. / Mu, W.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31922073 China
CitationJournal: J.Agric.Food Chem. / Year: 2022
Title: Crystal Structure of Levansucrase from the Gram-Negative Bacterium Brenneria Provides Insights into Its Product Size Specificity.
Authors: Xu, W. / Ni, D. / Hou, X. / Pijning, T. / Guskov, A. / Rao, Y. / Mu, W.
History
DepositionJul 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 11, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,25714
Polymers49,3971
Non-polymers1,86013
Water9,908550
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint3 kcal/mol
Surface area18190 Å2
Unit cell
Length a, b, c (Å)98.125, 98.125, 215.534
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-833-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Levansucrase


Mass: 49396.871 Da / Num. of mol.: 1 / Mutation: D68N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brenneria sp. EniD312 (bacteria) / Gene: BrE312_3941 / Production host: Escherichia coli (E. coli) / References: UniProt: G7LSK3, levansucrase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 562 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.18→84.98 Å / Num. obs: 161790 / % possible obs: 80.7 % / Redundancy: 38.1 % / CC1/2: 1 / Net I/σ(I): 18.8
Reflection shellResolution: 1.18→1.2 Å / Num. unique obs: 578 / CC1/2: 0.644 / % possible all: 5.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D47

4d47


Resolution: 1.35→84.98 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.306 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1498 6601 4.9 %RANDOM
Rwork0.1291 ---
obs0.1301 127550 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.82 Å2 / Biso mean: 15.974 Å2 / Biso min: 4.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.41 Å2-0 Å2
2---0.83 Å20 Å2
3---2.69 Å2
Refinement stepCycle: final / Resolution: 1.35→84.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 147 550 3973
Biso mean--30.03 32.91 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133560
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173251
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.6614837
X-RAY DIFFRACTIONr_angle_other_deg1.3921.5827547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88222.961179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51115518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.111517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
X-RAY DIFFRACTIONr_rigid_bond_restr4.65336811
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 471 -
Rwork0.187 9157 -
all-9628 -
obs--98.53 %

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