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- PDB-8qmf: Transketolase from Vibrio vulnificus in complex with thiamin pyro... -

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Basic information

Entry
Database: PDB / ID: 8qmf
TitleTransketolase from Vibrio vulnificus in complex with thiamin pyrophosphate
ComponentsTransketolase 2
KeywordsCYTOSOLIC PROTEIN / Transketolase / Infectious bacteria / Pentose phosphate pathway / Vibrio vulnificus
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase-like, pyrimidine-binding domain ...Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
NICKEL (II) ION / THIAMINE DIPHOSPHATE / Transketolase 2
Similarity search - Component
Biological speciesVibrio vulnificus YJ016 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBallut, L. / Georges, R.N. / Octobre, G. / Charmantray, F. / Doumeche, B.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: Protein Sci. / Year: 2024
Title: Structural determination and kinetic analysis of the transketolase from Vibrio vulnificus reveal unexpected cooperative behavior.
Authors: Georges, R.N. / Ballut, L. / Octobre, G. / Comte, A. / Hecquet, L. / Charmantray, F. / Doumeche, B.
History
DepositionSep 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transketolase 2
B: Transketolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,65119
Polymers147,9482
Non-polymers1,70317
Water12,881715
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13350 Å2
ΔGint-26 kcal/mol
Surface area41600 Å2
Unit cell
Length a, b, c (Å)69.230, 75.480, 130.390
Angle α, β, γ (deg.)90.000, 99.870, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transketolase 2


Mass: 73974.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus YJ016 (bacteria) / Gene: tkt2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MDD4

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Non-polymers , 5 types, 732 molecules

#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.1→34.95 Å / Num. obs: 76983 / % possible obs: 99.39 % / Redundancy: 3.19 % / Biso Wilson estimate: 35.13 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.087 / Net I/σ(I): 11.66
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.19 % / Mean I/σ(I) obs: 1.95 / Num. unique obs: 9913 / CC1/2: 0.675 / Rrim(I) all: 0.896 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.95 Å / SU ML: 0.2278 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.207 3849 5 %
Rwork0.1625 73109 -
obs0.1647 76958 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.59 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10356 0 103 715 11174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006610700
X-RAY DIFFRACTIONf_angle_d0.822914486
X-RAY DIFFRACTIONf_chiral_restr0.05031522
X-RAY DIFFRACTIONf_plane_restr0.00741910
X-RAY DIFFRACTIONf_dihedral_angle_d6.98951460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.2751380.25142619X-RAY DIFFRACTION99.32
2.13-2.150.31981440.24832733X-RAY DIFFRACTION99.65
2.15-2.180.28931420.23812700X-RAY DIFFRACTION99.75
2.18-2.220.25831440.23582731X-RAY DIFFRACTION99.69
2.22-2.250.31751400.22962659X-RAY DIFFRACTION99.57
2.25-2.280.23551440.21692740X-RAY DIFFRACTION99.69
2.28-2.320.25061420.21482690X-RAY DIFFRACTION99.33
2.32-2.360.24831400.20352675X-RAY DIFFRACTION99.54
2.36-2.40.27211430.21042711X-RAY DIFFRACTION99.65
2.4-2.450.24781410.19452679X-RAY DIFFRACTION99.47
2.45-2.50.2481420.18682699X-RAY DIFFRACTION99.51
2.5-2.550.25431440.18352733X-RAY DIFFRACTION99.62
2.55-2.610.24581420.18262690X-RAY DIFFRACTION99.44
2.61-2.680.22341420.17952700X-RAY DIFFRACTION99.54
2.68-2.750.24291410.18072680X-RAY DIFFRACTION99.65
2.75-2.830.21511440.17752729X-RAY DIFFRACTION99.69
2.83-2.920.25341430.16882724X-RAY DIFFRACTION99.62
2.92-3.030.22261420.17032706X-RAY DIFFRACTION99.34
3.03-3.150.20511430.16472714X-RAY DIFFRACTION99.51
3.15-3.290.19661430.16232706X-RAY DIFFRACTION99.58
3.29-3.470.22011420.15482707X-RAY DIFFRACTION99.23
3.47-3.680.17591430.14512713X-RAY DIFFRACTION99.34
3.68-3.970.16461430.13342715X-RAY DIFFRACTION98.96
3.97-4.370.15981430.1212722X-RAY DIFFRACTION99.34
4.37-50.15131440.12462741X-RAY DIFFRACTION99.24
5-6.290.18031440.15192730X-RAY DIFFRACTION98.76
6.29-34.950.18971460.14832763X-RAY DIFFRACTION97.78

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