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- PDB-8qkw: Crystal structure of Levansucrase from Pseudomonas syringae in co... -

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Basic information

Entry
Database: PDB / ID: 8qkw
TitleCrystal structure of Levansucrase from Pseudomonas syringae in complex with a tetravalent iminosugar
ComponentsGlutamate 5-kinase
KeywordsTRANSFERASE / inhibitor / complex / beta-propeller
Function / homologylevansucrase / levansucrase activity / Glycoside hydrolase, family 68 / Levansucrase/Invertase / carbohydrate utilization / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / : / Levansucrase Lscbeta
Function and homology information
Biological speciesPseudomonas syringae pv. actinidiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFerraroni, M. / Canovai, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Molecular Basis of Pseudomonas syringae pv actinidiae Levansucrase Inhibition by a Multivalent Iminosugar.
Authors: Cicchi, C. / Pazzagli, L. / Paoli, P. / Campigli, S. / Marchi, G. / Cardona, F. / Clemente, F. / Pavone, S. / Ferraroni, M. / Canovai, A. / Matassini, C. / Luti, S.
History
DepositionSep 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate 5-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8519
Polymers47,6911
Non-polymers6,1608
Water5,098283
1
A: Glutamate 5-kinase
hetero molecules

A: Glutamate 5-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,70318
Polymers95,3822
Non-polymers12,32116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)120.090, 63.990, 67.990
Angle α, β, γ (deg.)90.000, 103.496, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

21A-799-

HOH

31A-868-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate 5-kinase / Levansucrase


Mass: 47690.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GenBank accession number AOE59821.1
Source: (gene. exp.) Pseudomonas syringae pv. actinidiae (bacteria)
Gene: KPSA3_07534 / Plasmid: pNIK28 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V0R8Q9

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Non-polymers , 6 types, 291 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-VXT / 2-(hydroxymethyl)-1-[6-[4-[[3-[[3-[6-[(2~{S},3~{R},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidin-1-yl]hexyl]-1,2,3-triazol-4-yl]methoxy]-2,2-bis[[1-[6-[2-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidin-1-yl]hexyl]-1,2,3-triazol-4-yl]methoxymethyl]propoxy]methyl]-1,2,3-triazol-1-yl]hexyl]pyrrolidine-3,4-diol


Mass: 1321.608 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C61H108N16O16 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 21 % PEG 8000, 0.25 M sodium acetate, 0.1 M MES pH= 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→66.1 Å / Num. obs: 59642 / % possible obs: 98.6 % / Redundancy: 6.54 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.09 / Net I/σ(I): 12.87
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.65-1.696.670.9743780.7411.0521
1.69-1.740.75842320.8110.8241
1.74-1.790.61241530.8650.6681
1.79-1.840.45939820.9220.4981
1.84-1.90.32839510.9520.3571
1.9-1.970.24837060.9720.271
1.97-2.050.19436780.9830.211
2.05-2.130.15535560.9890.1681
2.13-2.220.13233680.990.1431
2.22-2.330.10732430.9920.1161
2.33-2.460.09931260.9940.1081
2.46-2.610.0929230.9940.0971
2.61-2.790.07727500.9960.0841
2.79-3.010.07125690.9960.0771
3.01-3.30.06423800.9960.071
3.3-3.690.05821350.9960.0631
3.69-4.260.05419410.9970.0581
4.26-5.210.05116110.9970.0561
5.21-7.370.05212490.9970.0571
7.37-66.10.0517110.9970.0561

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→40.003 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.562 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.08 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2971 4.982 %RANDOM
Rwork0.1554 56668 --
all0.157 ---
obs-59639 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.791 Å2
Baniso -1Baniso -2Baniso -3
1--0.614 Å20 Å2-0.358 Å2
2--0.806 Å20 Å2
3----0.018 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 95 283 3592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123462
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.674721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.192522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27310506
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.75810162
X-RAY DIFFRACTIONr_chiral_restr0.1560.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022718
X-RAY DIFFRACTIONr_nbd_refined0.2120.21543
X-RAY DIFFRACTIONr_nbtor_refined0.3210.22323
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2263
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.223
X-RAY DIFFRACTIONr_mcbond_it2.3232.151667
X-RAY DIFFRACTIONr_mcangle_it3.2593.8532087
X-RAY DIFFRACTIONr_scbond_it3.9942.6151795
X-RAY DIFFRACTIONr_scangle_it5.6044.5752624
X-RAY DIFFRACTIONr_lrange_it6.80924.425267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.6920.2542110.264157X-RAY DIFFRACTION97.8056
1.692-1.7380.2522430.2333985X-RAY DIFFRACTION97.7798
1.738-1.7880.2582110.2183923X-RAY DIFFRACTION98.1715
1.788-1.8430.2071820.1873806X-RAY DIFFRACTION98.1058
1.843-1.9040.2062010.1673735X-RAY DIFFRACTION98.4
1.904-1.970.181960.1533517X-RAY DIFFRACTION97.6591
1.97-2.0440.1861750.1483496X-RAY DIFFRACTION98.5503
2.044-2.1280.1781820.1463374X-RAY DIFFRACTION98.8327
2.128-2.2220.1541540.1483205X-RAY DIFFRACTION98.7651
2.222-2.330.1911660.1473069X-RAY DIFFRACTION99.0205
2.33-2.4560.1841530.1462984X-RAY DIFFRACTION99.2721
2.456-2.6040.1881540.1542749X-RAY DIFFRACTION99.0447
2.604-2.7830.2141520.1522611X-RAY DIFFRACTION99.2457
2.783-3.0050.1811130.152456X-RAY DIFFRACTION99.0744
3.005-3.290.1861260.1532245X-RAY DIFFRACTION99.4547
3.29-3.6750.188880.1452066X-RAY DIFFRACTION99.2169
3.675-4.2370.148910.1281837X-RAY DIFFRACTION99.6382
4.237-5.1750.148780.1221542X-RAY DIFFRACTION99.3865
5.175-7.2580.218640.1881199X-RAY DIFFRACTION99.0588
7.258-40.0030.202310.201709X-RAY DIFFRACTION98.2736

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