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Yorodumi- PDB-6kez: Crystal structure of GAPDH/CP12/PRK complex from Arabidopsis thaliana -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kez | ||||||
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Title | Crystal structure of GAPDH/CP12/PRK complex from Arabidopsis thaliana | ||||||
Components |
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Keywords | OXIDOREDUCTASE/TRANSFERASE/PROTEIN BINDING / glyceraldehyde-2-phosphate dehydrogenase / phosphoribulokinase / CP12 chloroplast / OXIDOREDUCTASE-TRANSFERASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information peptide cross-linking via L-cystine / phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / negative regulation of reductive pentose-phosphate cycle / cellular response to anoxia / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) / stromule / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity ...peptide cross-linking via L-cystine / phosphoribulokinase / phosphoribulokinase activity / supramolecular complex / negative regulation of reductive pentose-phosphate cycle / 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 / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / chloroplast envelope / thylakoid / cellular response to cold / chloroplast stroma / chloroplast thylakoid membrane / nickel cation binding / response to light stimulus / response to cold / chloroplast / glucose metabolic process / disordered domain specific binding / NAD binding / NADP binding / cellular response to heat / protein-macromolecule adaptor activity / protein-containing complex assembly / protein homotetramerization / copper ion binding / mRNA binding / protein-containing complex binding / enzyme binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Yu, A. / Xie, Y. / Li, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Plant Cell / Year: 2020 Title: Photosynthetic Phosphoribulokinase Structures: Enzymatic Mechanisms and the Redox Regulation of the Calvin-Benson-Bassham Cycle. Authors: Yu, A. / Xie, Y. / Pan, X. / Zhang, H. / Cao, P. / Su, X. / Chang, W. / Li, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kez.cif.gz | 797.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kez.ent.gz | 661.6 KB | Display | PDB format |
PDBx/mmJSON format | 6kez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kez_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6kez_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6kez_validation.xml.gz | 148.4 KB | Display | |
Data in CIF | 6kez_validation.cif.gz | 197.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/6kez ftp://data.pdbj.org/pub/pdb/validation_reports/ke/6kez | HTTPS FTP |
-Related structure data
Related structure data | 6kevC 6kewSC 6kexC 3rvdS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36592.750 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GAPA1, GAPA, At3g26650, MLJ15.4, MLJ15_5 / Production host: Escherichia coli (E. coli) References: UniProt: P25856, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) #2: Protein | Mass: 39514.785 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g32060, T12O21.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P25697, phosphoribulokinase #3: Protein | Mass: 8542.076 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CP12-2, At3g62410, T12C14.110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LZP9 #4: Chemical | ChemComp-NAD / #5: 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: 3 Å3/Da / Density % sol: 58.97 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 100mM HEPES, pH7.5, 100mM KCl, 15% polyethylene glycol 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 68615 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 55.99606247 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.56 |
Reflection shell | Resolution: 3.5→3.56 Å / Rmerge(I) obs: 0.554 / Num. unique obs: 3452 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RVD, 6KEW Resolution: 3.5→50 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.5→50 Å
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LS refinement shell | Resolution: 3.497→3.622 Å /
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