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- PDB-7jh0: Crystallographic structure of glyceraldehyde-3-phosphate dehydrog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jh0 | ||||||
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Title | Crystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Schistosoma mansoni | ||||||
![]() | (Glyceraldehyde-3-phosphate ...) x 2 | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boreiko, S. / Silva, M. / Iulek, J. | ||||||
![]() | ![]() Title: Structure determination and analyses of the GAPDH from the parasite Schistosoma mansoni, the first one from a platyhelminth. Authors: Boreiko, S. / Silva, M. / Iulek, 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 | ![]() | 511.5 KB | Display | ![]() |
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PDB format | ![]() | 422.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.4 KB | Display | ![]() |
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Full document | ![]() | 522.2 KB | Display | |
Data in XML | ![]() | 52.4 KB | Display | |
Data in CIF | ![]() | 69.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k9dS S: Starting model for refinement |
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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
-Glyceraldehyde-3-phosphate ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 36503.578 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P20287, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Protein | | Mass: 36455.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P20287, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) |
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-Non-polymers , 5 types, 210 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.54 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.12 M Ethylene glycols (0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 M pentaethyleneglycol) , 0.1 M Buffer system 1 pH 6.5 (0,1 M MES/Imidazole) and 30% ...Details: 0.12 M Ethylene glycols (0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 M pentaethyleneglycol) , 0.1 M Buffer system 1 pH 6.5 (0,1 M MES/Imidazole) and 30% Mix of precipitants (20% V/V Glicerol e 10% w/V PEG 40,000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.08 |
Reflection | Resolution: 2.51→57.76 Å / Num. obs: 51375 / % possible obs: 99.9 % / Redundancy: 21.57 % / CC1/2: 0.999 / Rrim(I) all: 0.172 / Net I/σ(I): 14.35 |
Reflection shell | Resolution: 2.51→2.57 Å / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3515 / CC1/2: 0.501 / Rrim(I) all: 2.654 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4K9D Resolution: 2.51→57.76 Å / Cross valid method: THROUGHOUT / σ(F): 1.87 / Phase error: 35.86 / Stereochemistry target values: TWIN_LSQ_F
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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: 173.41 Å2 / Biso mean: 74.0242 Å2 / Biso min: 35.66 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.51→57.76 Å
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LS refinement shell | Resolution: 2.51→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: -8.9134 Å / Origin y: 11.2973 Å / Origin z: -3.4192 Å
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Refinement TLS group |
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