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- PDB-3rvd: Crystal structure of the binary complex, obtained by soaking, of ... -
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Basic information
Entry | Database: PDB / ID: 3rvd | ||||||
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Title | Crystal structure of the binary complex, obtained by soaking, 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 / binary complex / 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 | ![]() ![]() ![]() | ||||||
![]() | Fermani, S. / Thumiger, A. / 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. / Tumigher, 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 | ![]() | 674.8 KB | Display | ![]() |
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PDB format | ![]() | 558 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.5 MB | Display | |
Data in XML | ![]() | 163 KB | Display | |
Data in CIF | ![]() | 213.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2lj9C ![]() 3qv1C ![]() 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36391.570 Da / Num. of mol.: 10 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.: 6 / Fragment: UNP residues 54-131 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.4 M ammonium sulphate, 0.1 M sodium citrate, 1 mM NAD, 3.125 mg/ml CP12 for soaking experiments, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→95.3 Å / Num. all: 119322 / Num. obs: 118509 / % possible obs: 96.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.587 / % possible all: 84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3K2B Resolution: 2.7→94.61 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3188319.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.8944 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→94.61 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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