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- PDB-6ynh: GAPDH purified from the supernatant of HEK293F cells: crystal for... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ynh | |||||||||
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Title | GAPDH purified from the supernatant of HEK293F cells: crystal form 4 of 4 | |||||||||
![]() | Glyceraldehyde-3-phosphate dehydrogenase![]() | |||||||||
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Function / homology | ![]() peptidyl-cysteine S-trans-nitrosylation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Roversi, P. / Lia, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid. Authors: Lia, A. / Dowle, A. / Taylor, C. / Santino, A. / Roversi, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 261.9 KB | Display | ![]() |
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PDB format | ![]() | 210.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yndSC ![]() 6yneC ![]() 6ynfC 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: 36179.230 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() References: UniProt: P04406, ![]() ![]() #2: Chemical | ChemComp-XPE / ![]() #3: 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: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Condition F9 of the MORPHEUS crystallisation screen, 0.12M MORPHEUS monosaccharides solution, 0.1M MORPHEUS Buffer System 3, 30% v/v MORPHEUS Precipitant Mix 1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.62→86.1 Å / Num. obs: 28210 / % possible obs: 71.3 % / Redundancy: 17.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.4 / Rrim(I) all: 0.41 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.62→2.89 Å / Redundancy: 17.3 % / Rmerge(I) obs: 2.47 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1409 / CC1/2: 0.464 / Rrim(I) all: 2.54 / % possible all: 14 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6YND Resolution: 2.621→86.1 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.368 Details: Automated non-crystallographic restraints were used throughout, including water molecules (assigned to each chain using CCP4-Sortwater). At each catalytic Cys152 site, a 0.5:0.5 occupancy ...Details: Automated non-crystallographic restraints were used throughout, including water molecules (assigned to each chain using CCP4-Sortwater). At each catalytic Cys152 site, a 0.5:0.5 occupancy ratio mixture of Cys and Cys S-Sulfonic acid was initially modelled in Fo-Fc residual density. At each Cys152 site, occupancies for Cys and Cys S-Sulfonic acid were refined and constrained so that they sum up to 1.000 plus or minus 0.005. External secondary structure restraints to PDB ID 6YND were used.
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Displacement parameters | Biso mean: 45.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.621→86.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.621→2.78 Å
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