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- PDB-7xzg: High resolution crystal Structure of Glyceraldehyde-3-Phosphate D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xzg | ||||||
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Title | High resolution crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Candida albicans complexed with NAD+ | ||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Glycolysis / Homotetramer | ||||||
Function / homology | ![]() yeast-form cell wall / : / fungal biofilm matrix / hyphal cell wall / adhesion of symbiont to host / fungal-type cell wall / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / biological process involved in interaction with host / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / extracellular matrix binding ...yeast-form cell wall / : / fungal biofilm matrix / hyphal cell wall / adhesion of symbiont to host / fungal-type cell wall / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / biological process involved in interaction with host / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / extracellular matrix binding / fibronectin binding / laminin binding / cell-matrix adhesion / glycolytic process / glucose metabolic process / NAD binding / extracellular vesicle / NADP binding / cell surface / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cao, H. / Meng, J. / Ren, Y. / Wan, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High resolution crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Candida albicans complexed with NAD+ Authors: Cao, H. / Meng, J. / Ren, Y. / Wan, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.6 KB | Display | ![]() |
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PDB format | ![]() | 229.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 59.3 KB | Display | |
Data in CIF | ![]() | 86.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pymS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 35908.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5ADM7, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 32.5% v/v mPEG 550, 0.1M Trisodium citrate, pH 5.4, 1.0M sodium chloride, 20mM Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.879→35.612 Å / Num. obs: 124242 / % possible obs: 99.3 % / Redundancy: 4.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.1652 / Net I/σ(I): 10.24 |
Reflection shell | Resolution: 1.879→1.947 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 12367 / CC1/2: 0.829 / % possible all: 99.28 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PYM Resolution: 1.879→35.612 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.77 / 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: 64.08 Å2 / Biso mean: 24.4586 Å2 / Biso min: 10.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.879→35.612 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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