+Open data
-Basic information
Entry | Database: PDB / ID: 3uje | ||||||
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Title | Asymmetric complex of human neuron specific enolase-3-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 / Resolution: 1.55 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 | 3uje.cif.gz | 360.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uje.ent.gz | 289.1 KB | Display | PDB format |
PDBx/mmJSON format | 3uje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uje_validation.pdf.gz | 483.7 KB | Display | wwPDB validaton report |
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Full document | 3uje_full_validation.pdf.gz | 494.5 KB | Display | |
Data in XML | 3uje_validation.xml.gz | 38 KB | Display | |
Data in CIF | 3uje_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/3uje ftp://data.pdbj.org/pub/pdb/validation_reports/uj/3uje | HTTPS FTP |
-Related structure data
Related structure data | 3uccC 3ucdC 3ujfC 3ujrC 3ujsC 1te6S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48570.656 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 |
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-Non-polymers , 5 types, 599 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-2PG / | #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-PEP / | #6: 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: 2.3 Å3/Da / Density % sol: 46.47 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 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: 1.55→50 Å / Num. obs: 112787 / % possible obs: 87.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1TE6 Resolution: 1.55→42.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.584 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0849 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 14.706 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→42.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.554→1.595 Å / Total num. of bins used: 20
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