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- PDB-9lhy: Crystal structure of a wild-type tagose isomerase (TsT4Ease WT) f... -

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Basic information

Entry
Database: PDB / ID: 9lhy
TitleCrystal structure of a wild-type tagose isomerase (TsT4Ease WT) from Thermotogota bacterium complex with Zn
ComponentsTagaturonate/fructuronate epimerase
KeywordsISOMERASE / tagose isomerase / Thermotogota bacterium / D-tagose / metal ion
Function / homologytagaturonate epimerase / racemase and epimerase activity, acting on hydroxy acids and derivatives / Tagaturonate/fructuronate epimerase / tagaturonate epimerase / Aldolase-type TIM barrel / metal ion binding / Tagaturonate/fructuronate epimerase
Function and homology information
Biological speciesThermotogota bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsWei, H.L. / Wang, Y.X. / Liu, W.D. / Zhu, L.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Protein Engineering of Tagatose 4-Epimerase for D-Tagatose Production.
Authors: Wang, Y. / Tan, Z. / Wei, H. / Zhang, N. / Wang, L. / Yang, Y. / Liu, W. / Zhu, L.
History
DepositionJan 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tagaturonate/fructuronate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2233
Polymers58,0921
Non-polymers1312
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.561, 83.278, 110.410
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 Tagaturonate/fructuronate epimerase / D-TagA/D-FruA epimerase


Mass: 58092.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotogota bacterium (bacteria) / Gene: uxaE, DHV12_03255
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A3D6D9W2, tagaturonate epimerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M Tris pH 8.5, 0.2 M Lithium sulfate monohydrate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.46→66.49 Å / Num. obs: 21070 / % possible obs: 92.7 % / Redundancy: 14.7 % / CC1/2: 0.979 / Χ2: 0.82 / Net I/σ(I): 7.5
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 8.6 % / Num. unique obs: 3250 / CC1/2: 0.31 / Χ2: 0.54

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→66.49 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2696 988 4.99 %
Rwork0.2429 --
obs0.2442 19818 87.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→66.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 2 88 4066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044124
X-RAY DIFFRACTIONf_angle_d0.7875573
X-RAY DIFFRACTIONf_dihedral_angle_d6.924552
X-RAY DIFFRACTIONf_chiral_restr0.047607
X-RAY DIFFRACTIONf_plane_restr0.005720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.590.33161400.30372678X-RAY DIFFRACTION89
2.59-2.750.33761290.3182430X-RAY DIFFRACTION80
2.75-2.960.31261610.28643048X-RAY DIFFRACTION100
2.96-3.260.33381600.27113035X-RAY DIFFRACTION100
3.26-3.730.3561000.35261900X-RAY DIFFRACTION62
3.73-4.70.24831280.23392515X-RAY DIFFRACTION81
4.7-66.490.21051700.18413224X-RAY DIFFRACTION99

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