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- PDB-8qj5: Crystal structure of the Levansucrase beta from Pseudomonas syrin... -

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Basic information

Entry
Database: PDB / ID: 8qj5
TitleCrystal structure of the Levansucrase beta from Pseudomonas syringae pv. actinidiae
ComponentsGlutamate 5-kinase
KeywordsTRANSFERASE / beta-propeller / levan / glycoside hydrolase
Function / homology
Function and homology information


levansucrase / levansucrase activity / carbohydrate utilization
Similarity search - Function
Glycoside hydrolase, family 68 / Levansucrase/Invertase / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily
Similarity search - Domain/homology
ACETATE ION / polyethylene glycol / PHOSPHATE ION / THIOCYANATE ION / Levansucrase Lscbeta
Similarity search - Component
Biological speciesPseudomonas syringae pv. actinidiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsFerraroni, M. / Peritore, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the Levansucrase beta from Pseudomonas syringae pv. actinidiae
Authors: Ferraroni, M. / Peritore, L. / Matassini, C. / Luti, S. / Cardona, F. / Paolo, P.
History
DepositionSep 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate 5-kinase
B: Glutamate 5-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,51416
Polymers95,6122
Non-polymers1,90214
Water11,512639
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-16 kcal/mol
Surface area30670 Å2
Unit cell
Length a, b, c (Å)57.610, 100.630, 77.930
Angle α, β, γ (deg.)90.00, 96.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate 5-kinase / Levansucrase


Mass: 47806.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GenBank Accession code AOE59821.1
Source: (gene. exp.) Pseudomonas syringae pv. actinidiae (bacteria)
Gene: KPSA3_07534 / Plasmid: pNIK28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V0R8Q9

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Non-polymers , 7 types, 653 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H62O15
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 100mM sodium thiocianate

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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: Jul 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→61.4 Å / Num. obs: 109338 / % possible obs: 99.7 % / Redundancy: 6.43 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.083 / Net I/σ(I): 14.89
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.63-1.676.531.0980810.7731.1861
1.67-1.720.87978630.8210.9581
1.72-1.770.70876150.8750.771
1.77-1.820.54874090.9220.5951
1.82-1.880.41371940.9540.4491
1.88-1.950.30569910.9690.3331
1.95-2.020.22467370.9840.2431
2.02-2.110.18265040.9880.1991
2.11-2.20.14261550.9920.1551
2.2-2.310.12159580.9940.1321
2.31-2.430.09956510.9960.1081
2.43-2.580.08653090.9960.0951
2.58-2.760.07450740.9970.0811
2.76-2.980.0646680.9970.0651
2.98-3.260.04943190.9980.0541
3.26-3.650.04139040.9980.0451
3.65-4.210.03534480.9980.0381
4.21-5.160.03129120.9990.0341
5.16-7.30.03322900.9990.0361
7.3-61.40.0312560.9990.0331

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→29.3 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.914 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19025 5420 5 %RANDOM
Rwork0.16109 ---
obs0.16256 103851 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.906 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.03 Å2
2--0.08 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.63→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6421 0 98 639 7158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.6449276
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7915851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18522.162370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.506151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.471545
X-RAY DIFFRACTIONr_chiral_restr0.1340.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025351
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0242.0823320
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8283.1124152
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4872.4193477
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.03729.9310475
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.632→1.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 403 -
Rwork0.267 7632 -
obs--99.83 %

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