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Yorodumi- PDB-5fh4: The structure of rat cytosolic PEPCK variant E89D in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fh4 | |||||||||
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Title | The structure of rat cytosolic PEPCK variant E89D in complex with beta-sulfopyruvate and GTP | |||||||||
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 / Resolution: 1.49 Å | |||||||||
Authors | Johnson, T.A. / Holyoak, T. | |||||||||
Funding support | United States, Canada, 2items
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Citation | Journal: Biochemistry / Year: 2016 Title: Utilization of Substrate Intrinsic Binding Energy for Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase. Authors: Johnson, T.A. / Mcleod, M.J. / Holyoak, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fh4.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fh4.ent.gz | 213.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fh4_validation.pdf.gz | 822.4 KB | Display | wwPDB validaton report |
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Full document | 5fh4_full_validation.pdf.gz | 825.3 KB | Display | |
Data in XML | 5fh4_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 5fh4_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/5fh4 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/5fh4 | HTTPS FTP |
-Related structure data
Related structure data | 5fh0C 5fh1C 5fh2C 5fh3C 5fh5C 3dt7S 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: 69485.633 Da / Num. of mol.: 1 / Mutation: e89d 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, 510 molecules
#2: Chemical | #3: Chemical | ChemComp-GTP / | #4: Chemical | ChemComp-SPV / | #5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43.5 % |
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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, 8MM MNCL2, 10mM GTP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.49→100 Å / Num. obs: 95906 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.088 / Χ2: 1.005 / Net I/av σ(I): 13.94 / Net I/σ(I): 13 / Num. measured all: 585490 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DT7 Resolution: 1.49→34.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2286 / WRfactor Rwork: 0.2044 / FOM work R set: 0.7929 / SU B: 3.747 / SU ML: 0.074 / SU R Cruickshank DPI: 0.0873 / SU Rfree: 0.0851 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 86.65 Å2 / Biso mean: 23.33 Å2 / Biso min: 11.47 Å2
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Refinement step | Cycle: final / Resolution: 1.49→34.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.49→1.529 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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