+Open data
-Basic information
Entry | Database: PDB / ID: 600000000 | |||||||||
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Title | Crystal structure of G6PD in complex with structural NADP | |||||||||
Components | Glucose-6-phosphate 1-dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / G6PD / NADP | |||||||||
Function / homology | Function and homology information 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 / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / 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 / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP metabolic process / pentose-phosphate shunt / glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / cholesterol biosynthetic process / erythrocyte maturation / centriolar satellite / negative regulation of reactive oxygen species metabolic process / glutathione metabolic process / regulation of neuron apoptotic process / substantia nigra development / TP53 Regulates Metabolic Genes / lipid metabolic process / cytoplasmic side of plasma membrane / response to organic cyclic compound / glucose metabolic process / cellular response to oxidative stress / NADP binding / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Rahighi, S. / Mochly Rosen, D. / Wakatsuki, S. | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator. Authors: Hwang, S. / Mruk, K. / Rahighi, S. / Raub, A.G. / Chen, C.H. / Dorn, L.E. / Horikoshi, N. / Wakatsuki, S. / Chen, J.K. / Mochly-Rosen, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e08.cif.gz | 226.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e08.ent.gz | 180.9 KB | Display | PDB format |
PDBx/mmJSON format | 6e08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/6e08 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/6e08 | HTTPS FTP |
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-Related structure data
Related structure data | 6e07C 2bhlS 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: 59332.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Production host: Escherichia coli K-12 (bacteria) References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+) | ||
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#2: Chemical | ChemComp-NAP / | ||
#3: Chemical | ChemComp-GOL / #4: 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: 2.39 Å3/Da / Density % sol: 48.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 20% w/v PEG 3350, 0.2 M potassium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 40413 / % possible obs: 95.3 % / Redundancy: 5.7 % / CC1/2: 1 / Rmerge(I) obs: 0.79 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3 / Num. unique obs: 5400 / CC1/2: 0.82 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BHL Resolution: 1.9→18.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.127 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.422 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→18.28 Å
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Refine LS restraints |
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