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Yorodumi- PDB-3qv1: Crystal structure of the binary complex of photosyntetic A4 glyce... -
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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. | ||||||
Components |
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Keywords | OXIDOREDUCTASE/PROTEIN BINDING / Rossmann fold / Calvin cycle / NAD / Chloroplast / OXIDOREDUCTASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information 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 / apoplast / reductive pentose-phosphate cycle / chloroplast envelope / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / cellular response to cold / chloroplast stroma / chloroplast thylakoid membrane / nickel cation binding / response to light stimulus / response to cold / chloroplast / glucose metabolic process / NAD binding / disordered domain specific binding / protein-macromolecule adaptor activity / cellular response to heat / NADP binding / protein homotetramerization / protein-containing complex assembly / 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 | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Thumiger, A. / Fermani, S. / Falini, G. / Marri, L. / Sparla, F. / Trost, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 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: Journal: Acta Crystallogr.,Sect.F / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qv1.cif.gz | 403.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qv1.ent.gz | 331.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/3qv1 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/3qv1 | HTTPS FTP |
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-Related structure data
Related structure data | 2lj9C 3rvdC 3k2bS 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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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.) Arabidopsis thaliana (thale cress) / Gene: At3g26650, GAPA, MLJ15.4, MLJ15_5 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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.) Arabidopsis thaliana (thale cress) / Gene: At3g62410, T12C14_110 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LZP9 |
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-Non-polymers , 5 types, 203 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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