+Open data
-Basic information
Entry | Database: PDB / ID: 3ucc | ||||||
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Title | Asymmetric complex of human neuron specific enolase-1-PGA/PEP | ||||||
Components | Gamma-enolase | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / gluconeogenesis / glycolytic process / perikaryon ...phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / gluconeogenesis / glycolytic process / perikaryon / magnesium ion binding / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Qin, J. / Chai, G. / Brewer, J. / Lovelace, L. / Lebioda, L. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2012 Title: Structures of asymmetric complexes of human neuron specific enolase with resolved substrate and product and an analogous complex with two inhibitors indicate subunit interaction and inhibitor cooperativity. Authors: Qin, J. / Chai, G. / Brewer, J.M. / Lovelace, L.L. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ucc.cif.gz | 326.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ucc.ent.gz | 257.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ucc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/3ucc ftp://data.pdbj.org/pub/pdb/validation_reports/uc/3ucc | HTTPS FTP |
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-Related structure data
Related structure data | 3ucdC 3ujeC 3ujfC 3ujrC 3ujsC 2akmS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 48017.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ENO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P09104, phosphopyruvate hydratase #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: 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: 2.43 Å3/Da / Density % sol: 49.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG4K, 0.2M MgCl2, 0.1M Tris-HCl, pH 8.5, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 131445 / % possible obs: 87.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.084 / Χ2: 3.407 / Net I/σ(I): 16.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AKM Resolution: 1.5→36.44 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.862 / WRfactor Rfree: 0.2329 / WRfactor Rwork: 0.1999 / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.884 / SU B: 3.76 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1322 / SU Rfree: 0.1037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 234.17 Å2 / Biso mean: 7.5783 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→36.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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