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- PDB-7ehr: Levansucrase from Brenneria sp. EniD 312 at 1.33 angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 7ehr
TitleLevansucrase from Brenneria sp. EniD 312 at 1.33 angstroms resolution
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / levansucrase
Similarity search - Component
Biological speciesBrenneria sp. EniD312 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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)51,64418
Polymers49,3981
Non-polymers2,24617
Water8,845491
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 area4410 Å2
ΔGint2 kcal/mol
Surface area18290 Å2
Unit cell
Length a, b, c (Å)98.000, 98.000, 213.539
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-793-

HOH

21A-883-

HOH

31A-1056-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Levansucrase


Mass: 49397.855 Da / Num. of mol.: 1
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 , 7 types, 508 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / 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: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.33→84.87 Å / Num. obs: 138038 / % possible obs: 90.3 % / Redundancy: 36.8 % / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/σ(I): 20.1
Reflection shellResolution: 1.33→1.4 Å / Redundancy: 16.1 % / Num. unique obs: 6204 / CC1/2: 0.706 / Rpim(I) all: 0.012 / % possible all: 34.5

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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: 1.33→84.8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.176 --RANDOM
Rwork0.164 ---
obs-138038 96.8 %-
Displacement parametersBiso max: 99.48 Å2 / Biso min: 8.09 Å2
Refinement stepCycle: LAST / Resolution: 1.33→84.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 144 491 3911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0183639
X-RAY DIFFRACTIONr_bond_other_d0.0010.023258
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.8594941
X-RAY DIFFRACTIONr_angle_other_deg1.1712.8637602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7545446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56124.121165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23515530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.961519
X-RAY DIFFRACTIONr_chiral_restr0.1140.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024046
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02749
X-RAY DIFFRACTIONr_mcbond_it1.4521.6571739
X-RAY DIFFRACTIONr_mcbond_other1.4211.6541738
X-RAY DIFFRACTIONr_mcangle_it1.8632.4912197
X-RAY DIFFRACTIONr_mcangle_other1.8632.4942198
X-RAY DIFFRACTIONr_scbond_it2.1932.0951900
X-RAY DIFFRACTIONr_scbond_other2.1892.0881885
X-RAY DIFFRACTIONr_scangle_other2.6182.9592720
X-RAY DIFFRACTIONr_long_range_B_refined3.45421.6174012
X-RAY DIFFRACTIONr_long_range_B_other3.01320.6853891
X-RAY DIFFRACTIONr_rigid_bond_restr2.67636897
LS refinement shellResolution: 1.332→1.367 Å /
Num. reflection% reflection
Rwork2001 -
obs-21.02 %

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