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- PDB-4gnm: Structure of rat cytosolic PEPCK Ld_2g in complex with oxalate and GTP -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gnm | ||||||
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Title | Structure of rat cytosolic PEPCK Ld_2g in complex with oxalate and GTP | ||||||
![]() | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | ||||||
![]() | LYASE / kinase / gluconeogenesis | ||||||
Function / homology | ![]() Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / 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 / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / 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 / 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 / response to lipid / cellular response to glucagon stimulus / response to starvation / cellular response to interleukin-1 / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / cellular response to cAMP / response to nutrient levels / cellular response to dexamethasone stimulus / response to activity / gluconeogenesis / cellular response to glucose stimulus / response to bacterium / response to insulin / lipid metabolic process / cellular response to insulin stimulus / glucose metabolic process / GDP binding / glucose homeostasis / cellular response to tumor necrosis factor / manganese ion binding / cellular response to hypoxia / peptidyl-serine phosphorylation / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Johnson, T.A. / Holyoak, T. | ||||||
![]() | ![]() Title: The {Omega}-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function. Authors: Johnson, T.A. / Holyoak, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.1 KB | Display | ![]() |
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PDB format | ![]() | 117.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 749.4 KB | Display | ![]() |
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Full document | ![]() | 753.8 KB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 46.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gmmC ![]() 4gmuC ![]() 4gmwC ![]() 4gmzC ![]() 4gnlC ![]() 4gnoC ![]() 4gnpC ![]() 4gnqC ![]() 3dt2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 68546.531 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP) |
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-Non-polymers , 5 types, 613 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/OXL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/OXL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GTP / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-OXL / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | RESIDUES 464-474 (ATAAAEHKGK |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 22-26% PEG3350, 0.1 M HEPES, pH 7.4, 10 mM manganese chloride, 10 mM GTP, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2011 Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→100 Å / Num. obs: 94980 / % possible obs: 96.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3DT2 Resolution: 1.5→26.66 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.891 / SU ML: 0.067 / SU R Cruickshank DPI: 0.0836 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 27.082 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→26.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.537 Å / Total num. of bins used: 20
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