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Yorodumi- PDB-5v9h: Structure of the H477R variant of rat cytosolic PEPCK in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v9h | ||||||
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Title | Structure of the H477R variant of rat cytosolic PEPCK in complex with phosphoglycolate and GDP. | ||||||
Components | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | ||||||
Keywords | LYASE / phosphoenolpyruvate carboxykinase | ||||||
Function / homology | Function and homology information Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / : / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity ...Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / : / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to fructose stimulus / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / cellular hypotonic response / cellular hypotonic salinity response / carboxylic acid binding / glyceraldehyde-3-phosphate biosynthetic process / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / cellular hyperosmotic response / positive regulation of memory T cell differentiation / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / response to lipid / response to starvation / cellular response to glucagon stimulus / positive regulation of lipid biosynthetic process / cellular response to interleukin-1 / cellular response to retinoic acid / cellular response to cAMP / cellular response to dexamethasone stimulus / response to nutrient levels / response to activity / gluconeogenesis / response to bacterium / cellular response to glucose stimulus / response to insulin / lipid metabolic process / cellular response to insulin stimulus / GDP binding / glucose metabolic process / glucose homeostasis / manganese ion binding / cellular response to tumor necrosis factor / cellular response to hypoxia / peptidyl-serine phosphorylation / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å | ||||||
Authors | Holyoak, T. / Cui, D.S. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Asymmetric Anchoring Is Required for Efficient Omega-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase. Authors: Cui, D.S. / Broom, A. / Mcleod, M.J. / Meiering, E.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 | 5v9h.cif.gz | 260 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v9h.ent.gz | 204.3 KB | Display | PDB format |
PDBx/mmJSON format | 5v9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/5v9h ftp://data.pdbj.org/pub/pdb/validation_reports/v9/5v9h | HTTPS FTP |
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-Related structure data
Related structure data | 5v95C 5v97C 5v9fC 5v9gC 3dtbS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 69518.711 Da / Num. of mol.: 2 / Mutation: H477R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Production host: Escherichia coli (E. coli) References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP) |
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-Non-polymers , 6 types, 303 molecules
#2: Chemical | ChemComp-1PE / | ||||||||
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#3: Chemical | ChemComp-MN / #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.21 Å3/Da / Density % sol: 44.32 % / Description: rods |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 24 - 34% PEG 3350 and 100mM HEPES, at pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 17, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→100 Å / Num. obs: 65917 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.054 / Rrim(I) all: 0.143 / Χ2: 1.074 / Net I/σ(I): 10.3 / Num. measured all: 458307 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DTB Resolution: 2.15→85.04 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.772 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.351 / ESU R Free: 0.249 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.7 Å2 / Biso mean: 46.667 Å2 / Biso min: 24.52 Å2
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Refinement step | Cycle: final / Resolution: 2.15→85.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.137→2.192 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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