+Open data
-Basic information
Entry | Database: PDB / ID: 5d1f | ||||||
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Title | Crystal structure of maize PDRP bound with AMP and Hg2+ | ||||||
Components | Pyruvate, phosphate dikinase regulatory protein, chloroplasticPyruvic acid | ||||||
Keywords | TRANSFERASE / PDRP / reversible phosphorylation / C4 photosynthesis / ADP-dependent protein kinase/Pi-dependent protein phosphatase | ||||||
Function / homology | Function and homology information [pyruvate, phosphate dikinase] kinase / [pyruvate, phosphate dikinase]-phosphate phosphotransferase / phosphotransferase activity, phosphate group as acceptor / chloroplast stroma / phosphorylation / protein serine/threonine kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Zea mays (maize) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å | ||||||
Authors | Jiang, L. / Chen, Z. | ||||||
Citation | Journal: Plant Physiol. / Year: 2016 Title: Structural Basis of Reversible Phosphorylation by Maize Pyruvate Orthophosphate Dikinase Regulatory Protein Authors: Jiang, L. / Chen, Y.B. / Zheng, J. / Chen, Z. / Liu, Y. / Tao, Y. / Wu, W. / Chen, Z. / Wang, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d1f.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d1f.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 5d1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/5d1f ftp://data.pdbj.org/pub/pdb/validation_reports/d1/5d1f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44727.297 Da / Num. of mol.: 1 / Fragment: UNP residues 38-426 Mutation: A106V, F238S, V266A, F271L, A310D, G335A, V371A, W375S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: PDRP1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q195N6, [pyruvate, phosphate dikinase] kinase, [pyruvate, phosphate dikinase]-phosphate phosphotransferase |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-HG / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.04 Å3/Da / Density % sol: 75.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: peg, dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. all: 13309 / Num. obs: 13309 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 217.2 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/av σ(I): 55.5 / Net I/σ(I): 55.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.4→48.68 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.884 / SU B: 15.532 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.523 / ESU R Free: 0.339 / 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: 47.392 Å2
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Refinement step | Cycle: 1 / Resolution: 3.4→48.68 Å
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Refine LS restraints |
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