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Yorodumi- PDB-4ywd: Structure of rat cytosolic pepck in complex with 2,3-Pyridine dic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ywd | |||||||||
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Title | Structure of rat cytosolic pepck in complex with 2,3-Pyridine dicarboxylic acid | |||||||||
Components | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | |||||||||
Keywords | LYASE / KINASE / GLUCONEOGENESIS | |||||||||
Function / homology | Function and homology information Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / protein serine kinase activity (using GTP as donor) / response to methionine / cellular response to potassium ion starvation / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process ...Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / protein serine kinase activity (using GTP as donor) / response to methionine / cellular response to potassium ion starvation / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / cellular response to fructose stimulus / cellular hypotonic response / response to lipid / carboxylic acid binding / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / cellular hyperosmotic response / glyceraldehyde-3-phosphate biosynthetic process / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / cellular response to glucagon stimulus / response to starvation / cellular response to interleukin-1 / cellular response to dexamethasone stimulus / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / cellular response to cAMP / response to nutrient levels / response to activity / gluconeogenesis / lipid metabolic process / cellular response to glucose stimulus / response to bacterium / response to insulin / cellular response to insulin stimulus / glucose metabolic process / GDP binding / glucose homeostasis / cellular response to tumor necrosis factor / cellular response to hypoxia / peptidyl-serine phosphorylation / manganese ion binding / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Balan, M.D. / Johnson, T.A. / Mcleod, M.J. / Lotosky, W.R. / Holyoak, T. | |||||||||
Funding support | United States, Canada, 2items
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Citation | Journal: Biochemistry / Year: 2015 Title: Inhibition and Allosteric Regulation of Monomeric Phosphoenolpyruvate Carboxykinase by 3-Mercaptopicolinic Acid. Authors: Balan, M.D. / Mcleod, M.J. / Lotosky, W.R. / Ghaly, M. / Holyoak, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ywd.cif.gz | 257.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ywd.ent.gz | 205.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ywd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ywd_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 4ywd_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 4ywd_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 4ywd_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/4ywd ftp://data.pdbj.org/pub/pdb/validation_reports/yw/4ywd | HTTPS FTP |
-Related structure data
Related structure data | 4yw8C 4yw9C 4ywbC 2qewS 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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Unit cell |
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-Components
#1: Protein | Mass: 69499.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-NTM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 25% PEG 3350, 0.1M HEPES PH 7.4,2 MM MNCL2, 1MM 2,3-PYRIDINE DICARBOXYLIC ACID, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K PH range: 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. obs: 33335 / % possible obs: 92.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.519 / % possible all: 63.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QEW Resolution: 2.1→57.63 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.932 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 50.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→57.63 Å
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Refine LS restraints |
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