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- PDB-8waa: Human transketolase soaked with donor ketose D-xylulose -

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Basic information

Entry
Database: PDB / ID: 8waa
TitleHuman transketolase soaked with donor ketose D-xylulose
ComponentsTransketolase
KeywordsTRANSFERASE / Complex
Function / homology
Function and homology information


xylulose 5-phosphate biosynthetic process / Insulin effects increased synthesis of Xylulose-5-Phosphate / Pentose phosphate pathway / transketolase / transketolase activity / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / glyceraldehyde-3-phosphate biosynthetic process / NFE2L2 regulates pentose phosphate pathway genes / regulation of growth ...xylulose 5-phosphate biosynthetic process / Insulin effects increased synthesis of Xylulose-5-Phosphate / Pentose phosphate pathway / transketolase / transketolase activity / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / glyceraldehyde-3-phosphate biosynthetic process / NFE2L2 regulates pentose phosphate pathway genes / regulation of growth / thiamine pyrophosphate binding / peroxisome / vesicle / nuclear body / calcium ion binding / endoplasmic reticulum membrane / magnesium ion binding / protein homodimerization activity / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
: / Transketolase, C-terminal domain / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain ...: / Transketolase, C-terminal domain / : / Transketolase signature 1. / Transketolase, thiamine diphosphate binding domain / Transketolase, N-terminal / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / 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
D-Glyceraldehyde / Chem-THD / Transketolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLiu, Z. / Dai, S. / Tittmann, K.
Funding support Germany, China, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR 1296/TP 3 Germany
National Natural Science Foundation of China (NSFC)32271305 China
CitationJournal: Acs Catalysis / Year: 2024
Title: Multifaceted Role of the Substrate Phosphate Group in Transketolase Catalysis
Authors: Liu, Z. / Xiao, C. / Lin, S. / Tittmann, K. / Dai, S.
History
DepositionSep 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 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: Transketolase
B: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,07633
Polymers139,2952
Non-polymers2,78131
Water21,5461196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15010 Å2
ΔGint26 kcal/mol
Surface area39090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.500, 86.550, 92.700
Angle α, β, γ (deg.)90.000, 93.850, 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 / Sugars , 2 types, 4 molecules AB

#1: Protein Transketolase


Mass: 69647.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TKT / Production host: Escherichia coli (E. coli) / References: UniProt: P29401
#3: Sugar ChemComp-3GR / D-Glyceraldehyde / GLYCERALDEHYDE / (2R)-2,3-DIHYDROXYPROPANAL


Type: D-saccharide / Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 1225 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-THD / 2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE / ({ALPHA,BETA}-DIHYDROXYETHYL)-THIAMIN DIPHOSPHATE


Mass: 484.358 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N4O9P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1196 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 13.5-15% PEG 6000 (w/v), 4% PEG 400 (v/v), 2 % glycerol (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 223490 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.1 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.96
Reflection shellResolution: 1.5→1.6 Å / Num. unique obs: 31820 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→46.25 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.4254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1805 9136 5 %
Rwork0.1566 173594 -
obs0.1578 182730 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.66 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9494 0 174 1196 10864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008510293
X-RAY DIFFRACTIONf_angle_d1.067613953
X-RAY DIFFRACTIONf_chiral_restr0.05591542
X-RAY DIFFRACTIONf_plane_restr0.01011829
X-RAY DIFFRACTIONf_dihedral_angle_d13.30933907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.28063000.25575696X-RAY DIFFRACTION97.97
1.52-1.530.29393000.24985689X-RAY DIFFRACTION97.84
1.53-1.550.25163000.23555700X-RAY DIFFRACTION97.91
1.55-1.570.2473020.22795745X-RAY DIFFRACTION97.86
1.57-1.590.25343040.21845778X-RAY DIFFRACTION98.8
1.59-1.620.24182990.20885673X-RAY DIFFRACTION98.52
1.62-1.640.25383050.2095783X-RAY DIFFRACTION98.59
1.64-1.660.23743030.19495792X-RAY DIFFRACTION98.77
1.66-1.690.21483030.19515746X-RAY DIFFRACTION98.65
1.69-1.720.22513040.19285775X-RAY DIFFRACTION98.69
1.72-1.750.25353030.20455766X-RAY DIFFRACTION98.8
1.75-1.780.24292990.19225675X-RAY DIFFRACTION97.85
1.78-1.810.22433030.18455752X-RAY DIFFRACTION97.8
1.81-1.850.21713050.17625799X-RAY DIFFRACTION99.3
1.85-1.890.19843060.16425813X-RAY DIFFRACTION99.19
1.89-1.930.18273050.16075783X-RAY DIFFRACTION99.22
1.93-1.980.1853050.15895804X-RAY DIFFRACTION99.4
1.98-2.040.19323060.1675814X-RAY DIFFRACTION99.46
2.04-2.10.17653070.15825822X-RAY DIFFRACTION99.43
2.1-2.160.18223060.15415820X-RAY DIFFRACTION99.37
2.16-2.240.19643060.15415823X-RAY DIFFRACTION99.48
2.24-2.330.17553060.14865810X-RAY DIFFRACTION99.48
2.33-2.440.17743080.14595849X-RAY DIFFRACTION99.47
2.44-2.560.17553010.14965718X-RAY DIFFRACTION97.89
2.56-2.730.16413090.15055872X-RAY DIFFRACTION99.6
2.73-2.940.16973080.14655845X-RAY DIFFRACTION99.74
2.94-3.230.16513080.1455857X-RAY DIFFRACTION99.73
3.23-3.70.15313100.13915898X-RAY DIFFRACTION99.66
3.7-4.660.14753080.12845837X-RAY DIFFRACTION98.99
4.66-46.250.15983070.14855860X-RAY DIFFRACTION97.29

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