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- PDB-6va0: Crystal structure of glucose-6-phosphate dehydrogenase W509A muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6va0 | ||||||
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Title | Crystal structure of glucose-6-phosphate dehydrogenase W509A mutant in complex with catalytic NADP+ | ||||||
![]() | Glucose-6-phosphate 1-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Dehydrogenase / NADP+ | ||||||
Function / homology | ![]() negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / glucose-6-phosphate dehydrogenase (NADP+) / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / NADPH regeneration ...negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / glucose-6-phosphate dehydrogenase (NADP+) / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / erythrocyte maturation / cholesterol biosynthetic process / centriolar satellite / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / substantia nigra development / glutathione metabolic process / TP53 Regulates Metabolic Genes / response to organic cyclic compound / lipid metabolic process / cytoplasmic side of plasma membrane / glucose metabolic process / NADP binding / cellular response to oxidative stress / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Horikoshi, N. / Mochly-Rosen, D. / Wakatsuki, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency. Authors: Horikoshi, N. / Hwang, S. / Gati, C. / Matsui, T. / Castillo-Orellana, C. / Raub, A.G. / Garcia, A.A. / Jabbarpour, F. / Batyuk, A. / Broweleit, J. / Xiang, X. / Chiang, A. / Broweleit, R. / ...Authors: Horikoshi, N. / Hwang, S. / Gati, C. / Matsui, T. / Castillo-Orellana, C. / Raub, A.G. / Garcia, A.A. / Jabbarpour, F. / Batyuk, A. / Broweleit, J. / Xiang, X. / Chiang, A. / Broweleit, R. / Vohringer-Martinez, E. / Mochly-Rosen, D. / Wakatsuki, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.4 KB | Display | ![]() |
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PDB format | ![]() | 155.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 348 KB | Display | ![]() |
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Full document | ![]() | 348.4 KB | Display | |
Data in XML | ![]() | 1.4 KB | Display | |
Data in CIF | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6va7C ![]() 6va8C ![]() 6va9C ![]() 6vaqC ![]() 6a08S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 59217.453 Da / Num. of mol.: 1 / Mutation: W509A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-NAP / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.91 Å3/Da / Density % sol: 79.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG4000, Magnesium chloride, AG1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→47.62 Å / Num. obs: 25692 / % possible obs: 97.2 % / Redundancy: 42.341 % / Biso Wilson estimate: 93.78 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.143 / Rrim(I) all: 0.145 / Χ2: 1.072 / Net I/σ(I): 34.75 / Num. measured all: 1087829 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6A08 Resolution: 3.1→47.62 Å / SU ML: 0.3364 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0013 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 94.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→47.62 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.2464109505 Å / Origin y: 95.359487288 Å / Origin z: 30.1231071187 Å
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Refinement TLS group | Selection details: all |