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Yorodumi- PDB-4enl: CRYSTAL STRUCTURE OF HOLOENZYME REFINED AT 1.9 ANGSTROMS RESOLUTI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4enl | ||||||
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Title | CRYSTAL STRUCTURE OF HOLOENZYME REFINED AT 1.9 ANGSTROMS RESOLUTION: TRIGONAL-BIPYRAMIDAL GEOMETRY OF THE CATION BINDING SITE | ||||||
Components | ENOLASE | ||||||
Keywords | CARBON-OXYGEN LYASE | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Lebioda, L. / Stec, B. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1989 Title: Crystal Structure of Holoenzyme Refined at 1.9 Angstroms Resolution: Trigonal-Bipyramidal Geometry of the Cation Binding Site Authors: Lebioda, L. / Stec, B. #1: Journal: Biochemistry / Year: 1991 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: Journal: Biochemistry / Year: 1991 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: Journal: J.Mol.Biol. / Year: 1990 Title: Refined Structure of Yeast Apo-Enolase at 2.25 Angstroms Resolution Authors: Stec, B. / Lebioda, L. #4: Journal: J.Biol.Chem. / Year: 1989 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. #5: Journal: Nature / Year: 1988 Title: Crystal Structure of Enolase Indicates that Enolase and Pyruvate Kinase Evolved from a Common Ancestor Authors: Lebioda, L. / Stec, B. #6: Journal: J.Mol.Biol. / Year: 1984 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4enl.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4enl.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 4enl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4enl_validation.pdf.gz | 379.9 KB | Display | wwPDB validaton report |
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Full document | 4enl_full_validation.pdf.gz | 397.3 KB | Display | |
Data in XML | 4enl_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4enl_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/4enl ftp://data.pdbj.org/pub/pdb/validation_reports/en/4enl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO 143 AND PRO 265 ARE CIS PROLINES. 2: RESIDUES GLY 41 - VAL 42 AND PRO 265 - LYS 269 ARE PROBABLY PARTIALLY DISORDERED. |
-Components
#1: Protein | Mass: 46690.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00924, phosphopyruvate hydratase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.39 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion / pH: 5 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 29393 / Num. measured all: 59713 / Rmerge(I) obs: 0.06 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.149 / Highest resolution: 1.9 Å Details: RESIDUES GLY 41 - VAL 42 AND PRO 265 - LYS 269 ARE PROBABLY PARTIALLY DISORDERED. | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 25916 / Rfactor all: 0.149 / Rfactor obs: 0.149 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 3.2 |