+Open data
-Basic information
Entry | Database: PDB / ID: 8wa9 | ||||||
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Title | Human transketolase soaked with donor ketose D-fructose | ||||||
Components | Transketolase | ||||||
Keywords | TRANSFERASE / 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 / glyceraldehyde-3-phosphate biosynthetic process / pentose-phosphate shunt / 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 / glyceraldehyde-3-phosphate biosynthetic process / pentose-phosphate shunt / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Liu, Z. / Tittmann, K. / Dai, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wa9.cif.gz | 358.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wa9.ent.gz | 230.6 KB | Display | PDB format |
PDBx/mmJSON format | 8wa9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/8wa9 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/8wa9 | HTTPS FTP |
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-Related structure data
Related structure data | 8wa7C 8wa8C 8waaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 BL21(DE3) (bacteria) / References: UniProt: P29401, transketolase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 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) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25 Å / Num. obs: 342211 / % possible obs: 94.2 % / Redundancy: 1.7 % / Biso Wilson estimate: 14.89 Å2 / CC1/2: 0.992 / Net I/σ(I): 5.29 |
Reflection shell | Resolution: 1.5→1.6 Å / Num. unique obs: 59465 / CC1/2: 0.615 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.43 Å / SU ML: 0.1584 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.952 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→24.43 Å
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Refine LS restraints |
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LS refinement shell |
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