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Yorodumi- PDB-4bba: Crystal structure of glucokinase regulatory protein complexed to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bba | ||||||
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Title | Crystal structure of glucokinase regulatory protein complexed to phosphate | ||||||
Components | GLUCOKINASE REGULATORY PROTEIN | ||||||
Keywords | PROTEIN-BINDING PROTEIN / GLUCOSE METABOLISM | ||||||
Function / homology | Function and homology information negative regulation of glucokinase activity / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis ...negative regulation of glucokinase activity / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis / enzyme inhibitor activity / response to glucose / protein import into nucleus / glucose homeostasis / carbohydrate binding / carbohydrate metabolic process / enzyme binding / mitochondrion / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Pautsch, A. / Stadler, N. / Loehle, A. / Lenter, M. / Rist, W. / Berg, A. / Glocker, L. / Nar, H. / Reinhart, D. / Heckel, A. ...Pautsch, A. / Stadler, N. / Loehle, A. / Lenter, M. / Rist, W. / Berg, A. / Glocker, L. / Nar, H. / Reinhart, D. / Heckel, A. / Schnapp, G. / Kauschke, S.G. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Crystal Structure of Glucokinase Regulatory Protein. Authors: Pautsch, A. / Stadler, N. / Loehle, A. / Rist, W. / Berg, A. / Glocker, L. / Nar, H. / Reinert, D. / Lenter, M. / Heckel, A. / Schnapp, G. / Kauschke, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bba.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bba.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/4bba ftp://data.pdbj.org/pub/pdb/validation_reports/bb/4bba | HTTPS FTP |
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-Related structure data
Related structure data | 4bb9SC 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: 69775.000 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDEST8 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q14397 |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | DOUBLE MUTANT K326T K327T CTERMINAL HIS TAG LEHHHHHH |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % / Description: NONE |
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Crystal grow | Details: 12-16MG/ML IN 25 MM HEPES PH 7.4, 50 MM KCL, 1 MM MGCL2, 2 MM DTT. 20% PEG 3350, 0.1 M TRIS PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→69 Å / Num. obs: 47132 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 17.09 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.92→1.96 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 6.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BB9 Resolution: 1.92→63.97 Å / Cor.coef. Fo:Fc: 0.9401 / Cor.coef. Fo:Fc free: 0.9283 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.117 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 18.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→63.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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