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Yorodumi- PDB-7zqk: Crystal structure of photosynthetic glyceraldehyde-3-phosphate de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zqk | ||||||
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Title | Crystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) complexed with NAD+ | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / Rossman-fold domain / Calvin-Benson cycle / pyridin dinucleotide cofactors | ||||||
Function / homology | Function and homology information supramolecular complex / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / reductive pentose-phosphate cycle / chloroplast / kinase binding / glucose metabolic process / NAD binding / NADP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Fermani, S. / Zaffagnini, M. / Lemaire, S.D. / Falini, G. / Fanti, S. / Rossi, J. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Redox Biol / Year: 2022 Title: Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH. Authors: Mattioli, E.J. / Rossi, J. / Meloni, M. / De Mia, M. / Marchand, C.H. / Tagliani, A. / Fanti, S. / Falini, G. / Trost, P. / Lemaire, S.D. / Fermani, S. / Calvaresi, M. / Zaffagnini, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zqk.cif.gz | 147.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zqk.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/7zqk ftp://data.pdbj.org/pub/pdb/validation_reports/zq/7zqk | HTTPS FTP |
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-Related structure data
Related structure data | 7zq3C 7zq4C 1rm4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38021.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Cell: chloroplast / Gene: GAPA / Production host: Escherichia coli (E. coli) References: UniProt: P50362, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2-1.6 M (NH4)2SO4, 0.1 M Tris-HCl / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 12, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→102.66 Å / Num. all: 46186 / Num. obs: 46186 / % possible obs: 99 % / Redundancy: 4 % / Rpim(I) all: 0.11 / Rrim(I) all: 0.237 / Rsym value: 0.208 / Net I/av σ(I): 2 / Net I/σ(I): 3.3 / Num. measured all: 186949 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RM4 Resolution: 2.2→42.42 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.065 / SU ML: 0.201 / SU R Cruickshank DPI: 0.3214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.84 Å2 / Biso mean: 38.564 Å2 / Biso min: 19.13 Å2
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Refinement step | Cycle: final / Resolution: 2.2→42.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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