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

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Basic information

Entry
Database: PDB / ID: 7eht
TitleLevansucrase from Brenneria sp. EniD 312
ComponentsLevansucrase
KeywordsTRANSFERASE / Levansucrase / fructosyltransferase / levan synthesis
Function / homologylevansucrase / levansucrase activity / Glycoside hydrolase, family 68 / Levansucrase/Invertase / carbohydrate utilization / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / metal ion binding / TRIETHYLENE GLYCOL / levansucrase
Function and homology information
Biological speciesBrenneria sp. EniD312 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
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)51,80120
Polymers49,3311
Non-polymers2,47119
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-36 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.974, 97.974, 214.220
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-836-

HOH

21A-1114-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Levansucrase


Mass: 49330.789 Da / Num. of mol.: 1 / Mutation: H327A
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, 544 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammounium sulfate, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→84.8 Å / Num. obs: 3547784 / % possible obs: 90.5 % / Redundancy: 38.8 % / Rpim(I) all: 0.028 / Net I/σ(I): 22.2
Reflection shellResolution: 1.45→1.51 Å / Num. unique obs: 91324 / Rpim(I) all: 0.486

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Processing

Software
NameVersionClassification
REFMAC5refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D47

4d47


Resolution: 1.45→84.8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19 --RANDOM
Rwork0.172 ---
obs-108757 90.5 %-
Displacement parametersBiso max: 101.94 Å2 / Biso min: 10.27 Å2
Refinement stepCycle: LAST / Resolution: 1.45→84.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 157 525 3953
LS refinement shellResolution: 1.45→1.51 Å / % reflection obs: 66.3 %

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