+Open data
-Basic information
Entry | Database: PDB / ID: 6ioj | ||||||
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Title | Glyceraldehyde-3-phosphate dehydrogenase A (apo-form) | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase A | ||||||
Keywords | CYTOSOLIC PROTEIN / dehydrogenase | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Wang, H. / Sun, H. / Wang, M. | ||||||
Funding support | Hong Kong, 1items
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Citation | Journal: Chem Sci / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ioj.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ioj.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ioj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/6ioj ftp://data.pdbj.org/pub/pdb/validation_reports/io/6ioj | HTTPS FTP |
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-Related structure data
Related structure data | 6io4C 6io6C 1gadS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: gapA, b1779, JW1768 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A9B2, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.15M Malic acid, PEG3350 25% / 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: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å | ||||||||||||||||||||||||
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: 0.97917 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.29→47.79 Å / Num. obs: 26233 / % possible obs: 99.6 % / Redundancy: 25.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.022 / Rrim(I) all: 0.111 / Net I/σ(I): 19.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GAD Resolution: 2.29→42.741 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.52 Å2 / Biso mean: 69.8275 Å2 / Biso min: 35.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→42.741 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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