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- PDB-1nel: FLUORIDE INHIBITION OF YEAST ENOLASE: CRYSTAL STRUCTURE OF THE EN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nel | ||||||
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Title | FLUORIDE INHIBITION OF YEAST ENOLASE: CRYSTAL STRUCTURE OF THE ENOLASE-MG2+-F--PI COMPLEX AT 2.6-ANGSTROMS RESOLUTION | ||||||
![]() | ENOLASE | ||||||
![]() | CARBON-OXYGEN LYASE | ||||||
Function / homology | ![]() Gluconeogenesis / regulation of vacuole fusion, non-autophagic / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding ...Gluconeogenesis / regulation of vacuole fusion, non-autophagic / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding / mitochondrion / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Lebioda, L. / Zhang, E. / Lewinski, K. / Brewer, M.J. | ||||||
![]() | ![]() Title: Fluoride inhibition of yeast enolase: crystal structure of the enolase-Mg(2+)-F(-)-Pi complex at 2.6 A resolution. Authors: Lebioda, L. / Zhang, E. / Lewinski, K. / Brewer, J.M. #1: ![]() Title: Mechanism of Enolase: The Crystal Structure of Enolase-Mg2+-Phosphoglycerate(Slash) Phosphoenolpyruvate Complex at 2.2-Angstroms Resolution Authors: Lebioda, L. / Stec, B. #2: ![]() Title: Inhibition of Enolase: The Crystal Structures of Enolase-Ca2+-Phosphoglycerate and Enolase-Zn2+-Phosphoglycolate Complexes at 2.2-Angstroms Resolution Authors: Lebioda, L. / Stec, B. / Brewer, J.M. / Tykarska, E. #3: ![]() Title: Refined Structure of Yeast Apo-Enolase at 2.25 Angstroms Resolution Authors: Stec, B. / Lebioda, L. #4: ![]() Title: Crystal Structure of Holoenzyme Refined at 1.9 Angstroms Resolution: Trigonal-Bipyramidal Geometry of the Cation Binding Site Authors: Lebioda, L. / Stec, B. #5: ![]() Title: The Structure of Yeast Enolase at 2.25-Angstroms Resolution. An 8-Fold Beta+Alpha-Barrel with a Novel Beta Beta Alpha Alpha (Beta Alpha)6 Topology Authors: Lebioda, L. / Stec, B. / Brewer, J.M. #6: ![]() Title: Crystal Structure of Enolase Indicates that Enolase and Pyruvate Kinase Evolved from a Common Ancestor Authors: Lebioda, L. / Stec, B. #7: ![]() Title: Crystallization and Preliminary Crystallographic Data for a Tetragonal Form of Yeast Enolase Authors: Lebioda, L. / Brewer, J.M. | ||||||
History |
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Remark 700 | SHEET THE SHEET PRESENTED AS *BAR* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *BAR* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THERE IS A SMALL STRAND BONDED TO THE END OF STRAND 1 OF THE BARREL. THIS SMALL STRAND STRAND AND STRAND 1 ARE PRESENTED AS SHEET S1. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.8 KB | Display | ![]() |
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PDB format | ![]() | 77.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383 KB | Display | ![]() |
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Full document | ![]() | 430.1 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 143 / 2: CIS PROLINE - PRO 265 PROBABLY PARTIALLY DISORDERED. 3: RESIDUES PRO 265 - LYS 269 ARE PROBABLY PARTIALLY DISORDERED. |
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Components
#1: Protein | Mass: 46690.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00924, phosphopyruvate hydratase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-F / |
#5: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.29 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.59 Å / Num. obs: 17176 / Num. measured all: 63663 / Rmerge(I) obs: 0.063 |
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Reflection shell | *PLUS Highest resolution: 2.59 Å / Lowest resolution: 2.66 Å / % possible obs: 68 % |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2.6 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Highest resolution: 2.6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Num. reflection obs: 15142 / σ(F): 3 / Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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