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Yorodumi- PDB-4gnl: Structure of rat cytosolic PEPCK Ld_2g in complex with PEP and GDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gnl | ||||||
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Title | Structure of rat cytosolic PEPCK Ld_2g in complex with PEP and GDP | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Johnson, T.A. / Holyoak, T. | ||||||
Citation | Journal: Biochemistry / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gnl.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gnl.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 4gnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gnl_validation.pdf.gz | 854.2 KB | Display | wwPDB validaton report |
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Full document | 4gnl_full_validation.pdf.gz | 857.5 KB | Display | |
Data in XML | 4gnl_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 4gnl_validation.cif.gz | 39.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/4gnl ftp://data.pdbj.org/pub/pdb/validation_reports/gn/4gnl | HTTPS FTP |
-Related structure data
Related structure data | 4gmmC 4gmuC 4gmwC 4gmzC 4gnmC 4gnoC 4gnpC 4gnqC 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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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.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP) |
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-Non-polymers , 5 types, 379 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-GDP / | #5: Chemical | ChemComp-PEP / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES 464-474 (ATAAAEHKGK |
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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: 2.25 Å3/Da / Density % sol: 45.39 % |
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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 GDP, 10 mM PEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.15 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2012 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: 1.15 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. obs: 68183 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.073 / Χ2: 1.071 / Net I/σ(I): 12.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: PDB ENTRY 3DTB Resolution: 1.7→38.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2509 / WRfactor Rwork: 0.2093 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8312 / SU B: 2.561 / SU ML: 0.084 / SU R Cruickshank DPI: 0.115 / SU Rfree: 0.1148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.52 Å2 / Biso mean: 30.8166 Å2 / Biso min: 16.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→38.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.747 Å / Total num. of bins used: 20
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