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- PDB-3qv1: Crystal structure of the binary complex of photosyntetic A4 glyce... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qv1 | ||||||
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Title | Crystal structure of the binary complex of photosyntetic A4 glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with cp12-2, both from Arabidopsis thaliana. | ||||||
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![]() | OXIDOREDUCTASE/PROTEIN BINDING / Rossmann fold / Calvin cycle / NAD / Chloroplast / OXIDOREDUCTASE-PROTEIN BINDING complex | ||||||
Function / homology | ![]() peptide cross-linking via L-cystine / negative regulation of reductive pentose-phosphate cycle / supramolecular complex / cellular response to anoxia / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / stromule / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / chloroplast membrane / response to sucrose ...peptide cross-linking via L-cystine / negative regulation of reductive pentose-phosphate cycle / supramolecular complex / cellular response to anoxia / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / stromule / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity / chloroplast membrane / response to sucrose / reductive pentose-phosphate cycle / apoplast / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast envelope / cellular response to cold / chloroplast stroma / nickel cation binding / chloroplast thylakoid membrane / response to light stimulus / response to cold / chloroplast / glucose metabolic process / NAD binding / disordered domain specific binding / protein-macromolecule adaptor activity / NADP binding / cellular response to heat / protein-containing complex assembly / protein homotetramerization / copper ion binding / mRNA binding / protein-containing complex binding / enzyme binding / protein homodimerization activity / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thumiger, A. / Fermani, S. / Falini, G. / Marri, L. / Sparla, F. / Trost, P. | ||||||
![]() | ![]() Title: Conformational Selection and Folding-upon-binding of Intrinsically Disordered Protein CP12 Regulate Photosynthetic Enzymes Assembly. Authors: Fermani, S. / Trivelli, X. / Sparla, F. / Thumiger, A. / Calvaresi, M. / Marri, L. / Falini, G. / Zerbetto, F. / Trost, P. #1: ![]() Title: Structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (isoform A4) from Arabidopsis thaliana in complex with NAD. Authors: Fermani, S. / Sparla, F. / Marri, L. / Thumiger, A. / Pupillo, P. / Falini, G. / Trost, 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 | ![]() | 403.1 KB | Display | ![]() |
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PDB format | ![]() | 331.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 78.5 KB | Display | |
Data in CIF | ![]() | 104.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2lj9C ![]() 3rvdC ![]() 3k2bS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 36391.570 Da / Num. of mol.: 6 / Fragment: UNP residues 60-396 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P25856, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) #2: Protein | Mass: 8754.368 Da / Num. of mol.: 3 / Fragment: UNP residues 54-131 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 203 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAD / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15% (w/v) PEG 4K, 0.6 M NaCl, 1 mM NAD and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2→34.2 Å / Num. all: 168053 / Num. obs: 163587 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1.3 / Num. unique all: 24070 / Rsym value: 0.716 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3K2B Resolution: 2→34.2 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.434 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.638 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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