+Open data
-Basic information
Entry | Database: PDB / ID: 2cxn | ||||||
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Title | Crystal structure of mouse AMF / phosphate complex | ||||||
Components | Glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | Function and homology information glycolytic process through glucose-6-phosphate / Glycolysis / Gluconeogenesis / TP53 Regulates Metabolic Genes / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / canonical glycolysis ...glycolytic process through glucose-6-phosphate / Glycolysis / Gluconeogenesis / TP53 Regulates Metabolic Genes / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / canonical glycolysis / monosaccharide binding / erythrocyte homeostasis / ciliary membrane / positive regulation of immunoglobulin production / response to testosterone / mesoderm formation / response to immobilization stress / response to cadmium ion / response to muscle stretch / Neutrophil degranulation / positive regulation of endothelial cell migration / cytokine activity / gluconeogenesis / response to progesterone / glycolytic process / growth factor activity / response to estradiol / myelin sheath / glucose homeostasis / in utero embryonic development / negative regulation of neuron apoptotic process / learning or memory / ubiquitin protein ligase binding / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å | ||||||
Authors | Tanaka, N. / Haga, A. / Naba, N. / Shiraiwa, K. / Kusakabe, Y. / Hashimoto, K. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal structures of mouse autocrine motility factor in complex with carbohydrate phosphate inhibitors provide insight into structure-activity relationship of the inhibitors Authors: Tanaka, N. / Haga, A. / Naba, N. / Shiraiwa, K. / Kusakabe, Y. / Hashimoto, K. / Funasaka, T. / Nagase, H. / Raz, A. / Nakamura, K.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cxn.cif.gz | 251.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cxn.ent.gz | 199.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cxn_validation.pdf.gz | 390.1 KB | Display | wwPDB validaton report |
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Full document | 2cxn_full_validation.pdf.gz | 393.7 KB | Display | |
Data in XML | 2cxn_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 2cxn_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/2cxn ftp://data.pdbj.org/pub/pdb/validation_reports/cx/2cxn | HTTPS FTP |
-Related structure data
Related structure data | 2cvpC 2cxoC 2cxpC 2cxqC 2cxrC 2cxsC 2cxtC 2cxuC 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: 62693.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P06745, glucose-6-phosphate isomerase #2: Chemical | ChemComp-PO4 / | #3: Chemical | ChemComp-GOL / #4: 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Cacodylate, PEG8000, NaAcetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→40 Å / Num. obs: 215161 / % possible obs: 96.1 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.902 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.502 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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