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- PDB-7ehs: Levansucrase from Brenneria sp. EniD 312 -

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Basic information

Entry
Database: PDB / ID: 7ehs
TitleLevansucrase from Brenneria sp. EniD 312
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, five-bladed beta-propellor domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / levansucrase
Similarity search - Component
Biological speciesBrenneria sp. EniD312 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsXu, W. / Ni, D.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
DepositionMar 30, 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

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Assembly

Deposited unit
A: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,60520
Polymers49,4141
Non-polymers2,19119
Water10,160564
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Dynamic light scattering confirms monomeric solution state
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint5 kcal/mol
Surface area18580 Å2
Unit cell
Length a, b, c (Å)98.314, 98.314, 216.475
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-786-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Levansucrase /


Mass: 49413.855 Da / Num. of mol.: 1 / Mutation: A154S
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

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Non-polymers , 5 types, 583 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.25 Å3/Da / Density % sol: 62.15 %
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: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.34→85.15 Å / Num. obs: 80004 / % possible obs: 94.6 % / Redundancy: 39 % / Rpim(I) all: 0.025 / Net I/σ(I): 17.4
Reflection shellResolution: 1.34→1.39 Å / Num. unique obs: 14170 / Rpim(I) all: 0.456 / % possible all: 82.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D47

4d47


Resolution: 1.6→85.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1697 / WRfactor Rwork: 0.1473 / FOM work R set: 0.8866 / SU B: 1.43 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0734 / SU Rfree: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 3686 5 %RANDOM
Rwork0.1572 ---
obs0.1584 69526 89.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.32 Å2 / Biso mean: 18.853 Å2 / Biso min: 8.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.6→85.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 149 564 3994
Biso mean--39.55 33.62 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133593
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173238
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.6514881
X-RAY DIFFRACTIONr_angle_other_deg1.4431.5737566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3985449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55222.818181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07815531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7081518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02746
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 121 -
Rwork0.218 2280 -
all-2401 -
obs--40.03 %

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