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- PDB-1m53: CRYSTAL STRUCTURE OF ISOMALTULOSE SYNTHASE (PALI) FROM KLEBSIELLA... -

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Basic information

Entry
Database: PDB / ID: 1m53
TitleCRYSTAL STRUCTURE OF ISOMALTULOSE SYNTHASE (PALI) FROM KLEBSIELLA SP. LX3
ComponentsIsomaltulose Synthase
KeywordsISOMERASE / KLEBSIELLA SP. LX3 / ISOMALTULOSE SYNTHASE / SUCROSE ISOMERIZATION
Function / homology
Function and homology information


alpha-amylase activity / oligosaccharide catabolic process
Similarity search - Function
: / Alpha-amylase SusG C-terminal domain / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...: / Alpha-amylase SusG C-terminal domain / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Isomaltulose synthase
Similarity search - Component
Biological speciesKlebsiella sp. LX3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, N. / Swaminathan, K.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Isomaltulose synthase (PalI) of Klebsiella sp. LX3. Crystal structure and implication of mechanism
Authors: Zhang, D. / Li, N. / Lok, S.M. / Zhang, L.-H. / Swaminathan, K.
#1: Journal: APPL.ENVIRON.MICROBIOL. / Year: 2002
Title: Isomaltulose Synthase from Klebsiella sp. Strain LX3: Gene Cloning and Characterization and Engineering of Thermostability
Authors: Zhang, D.-H. / Li, X.-Z. / Zhang, L.-H.
History
DepositionJul 8, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isomaltulose Synthase


Theoretical massNumber of molelcules
Total (without water)67,2521
Polymers67,2521
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.239, 94.153, 111.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isomaltulose Synthase


Mass: 67251.797 Da / Num. of mol.: 1 / Fragment: residues 29-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella sp. LX3 (bacteria) / Gene: PalI / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8KR84, isomaltulose synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.31 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M SODIUM CACODYLATE, 0.2M AMMONIUM SULPHATE, 30%(W/V) PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1150 mM1dropNaCl
210 mMHEPES1droppH7.5
31 mMdithiothreitol1drop
410 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2002
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 32456 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Redundancy: 6.1 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.053 / Net I/σ(I): -3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rsym value: 0.269 / % possible all: 96.6
Reflection
*PLUS
Num. obs: 29756 / Num. measured all: 199659 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.26

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE: 1UOK

1uok


Resolution: 2.2→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 264716.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2931 10 %RANDOM
Rwork0.194 ---
obs0.194 29356 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.9159 Å2 / ksol: 0.440529 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1--8.33 Å20 Å20 Å2
2--13.63 Å20 Å2
3----5.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 0 303 4951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.2→2.33 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 468 11.1 %
Rwork0.221 3757 -
obs--81.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Lowest resolution: 2.28 Å

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