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- PDB-6frw: X-ray structure of the levansucrase from Erwinia tasmaniensis -

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Basic information

Entry
Database: PDB / ID: 6frw
TitleX-ray structure of the levansucrase from Erwinia tasmaniensis
ComponentsLevansucrase (Beta-D-fructofuranosyl transferase)
KeywordsTRANSFERASE / Fructosyltransferase / Sucrose hydrolase / Fructans production
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
Biological speciesErwinia tasmaniensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPolsinelli, I. / Salomone-Stagni, M. / Caliandro, R. / Demitri, N. / Benini, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Free University of Bolzano1440 Italy
CitationJournal: Int. J. Biol. Macromol. / Year: 2019
Title: Comparison of the Levansucrase from the epiphyte Erwinia tasmaniensis vs its homologue from the phytopathogen Erwinia amylovora.
Authors: Polsinelli, I. / Caliandro, R. / Salomone-Stagni, M. / Demitri, N. / Rejzek, M. / Field, R.A. / Benini, S.
History
DepositionFeb 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Levansucrase (Beta-D-fructofuranosyl transferase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,83311
Polymers45,9921
Non-polymers84110
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-93 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.493, 128.493, 58.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Levansucrase (Beta-D-fructofuranosyl transferase)


Mass: 45992.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia tasmaniensis (bacteria) / Gene: lsc, ETA_34670 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2VCC3, levansucrase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% Glycerol, 14% PEG 4000, 1.5mM Manganese(II) chloride tetrahydrate, 1.5 mM Cobalt(II) chloride hexahydrate , 1.5 mM Nickel(II) chloride hexahydrate, 1.5 mM Zinc acetate dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.43 Å / Num. obs: 76050 / % possible obs: 99.65 % / Redundancy: 2 % / Net I/σ(I): 14.64
Reflection shellResolution: 1.52→1.574 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→41.147 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.42
RfactorNum. reflection% reflection
Rfree0.2088 3808 5.02 %
Rwork0.1793 --
obs0.1807 75870 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.42 Å2 / Biso mean: 29.6202 Å2 / Biso min: 16.19 Å2
Refinement stepCycle: final / Resolution: 1.52→41.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 101 402 3750
Biso mean--46.34 36.84 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053536
X-RAY DIFFRACTIONf_angle_d0.84843
X-RAY DIFFRACTIONf_chiral_restr0.054513
X-RAY DIFFRACTIONf_plane_restr0.005635
X-RAY DIFFRACTIONf_dihedral_angle_d13.4022111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.52-1.53920.42431380.37352620275899
1.5392-1.55950.36881490.35232604275399
1.5595-1.58090.40231560.32892583273999
1.5809-1.60350.37841250.32312647277299
1.6035-1.62740.39611430.30832639278299
1.6274-1.65280.31761460.304226222768100
1.6528-1.67990.27681470.27326332780100
1.6799-1.70890.30651390.262626302769100
1.7089-1.740.27721470.249126342781100
1.74-1.77340.28271290.229726532782100
1.7734-1.80960.23071510.218426402791100
1.8096-1.8490.25491130.204326592772100
1.849-1.8920.22341500.1926602810100
1.892-1.93930.21761410.181726412782100
1.9393-1.99170.22151210.177726642785100
1.9917-2.05030.20741540.178226522806100
2.0503-2.11650.22391380.176926532791100
2.1165-2.19220.17011330.151926872820100
2.1922-2.27990.16681450.154626702815100
2.2799-2.38370.1671470.144226632810100
2.3837-2.50930.17841390.145426772816100
2.5093-2.66650.20231260.153727302856100
2.6665-2.87240.18361470.148726832830100
2.8724-3.16130.18831320.15827292861100
3.1613-3.61850.18091420.153127442886100
3.6185-4.5580.16861500.14322759290999
4.558-41.16180.19181600.18062884304499

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