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- PDB-6io6: Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A at non-ca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6io6 | ||||||
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Title | Silver-bound Glyceraldehyde-3-phosphate dehydrogenase A at non-catalytic site | ||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase A | ||||||
![]() | CYTOSOLIC PROTEIN / silver / dehydrogenase | ||||||
Function / homology | ![]() glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, H. / Sun, H. / Wang, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Antimicrobial silver targets glyceraldehyde-3-phosphate dehydrogenase in glycolysis ofE. coli. Authors: Wang, H. / Wang, M. / Yang, X. / Xu, X. / Hao, Q. / Yan, A. / Hu, M. / Lobinski, R. / Li, H. / Sun, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.3 KB | Display | ![]() |
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PDB format | ![]() | 107.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6io4C ![]() 6iojC ![]() 1gadS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35287.102 Da / Num. of mol.: 1 / Mutation: D79G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: gapA, b1779, JW1768 / Production host: ![]() ![]() References: UniProt: P0A9B2, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Malic acid, PEG3350 20% / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Nitrogen flow / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2018 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→48.32 Å / Num. obs: 17924 / % possible obs: 99.9 % / Redundancy: 26.8 % / CC1/2: 0.973 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.051 / Rrim(I) all: 0.256 / Net I/σ(I): 8.8 / Num. measured all: 480506 / Scaling rejects: 2808 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GAD Resolution: 2.64→48.321 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.89 / Stereochemistry target values: ML
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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 max: 153.15 Å2 / Biso mean: 83.4904 Å2 / Biso min: 39.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.64→48.321 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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