[English] 日本語
Yorodumi- PDB-1ebh: OCTAHEDRAL COORDINATION AT THE HIGH AFFINITY METAL SITE IN ENOLAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ebh | ||||||
---|---|---|---|---|---|---|---|
Title | OCTAHEDRAL COORDINATION AT THE HIGH AFFINITY METAL SITE IN ENOLASE; CRYSTALLOGRAPHIC ANALYSIS OF THE MG++-ENZYME FROM YEAST AT 1.9 ANGSTROMS RESOLUTION | ||||||
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 | Wedekind, J.E. / Reed, G.H. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Octahedral coordination at the high-affinity metal site in enolase: crystallographic analysis of the MgII--enzyme complex from yeast at 1.9 A resolution. Authors: Wedekind, J.E. / Reed, G.H. / Rayment, I. #1: Journal: Biochemistry / Year: 1994 Title: Chelation of Ser 39 to Mg++ Latches a Gate at the Active Site of Enolase: Structure of the Bis Mg++ Complex of Yeast Enolase and the Intermediate, Phosphonoacetohydroxamate, at 2.1 Angstroms Resolution Authors: Wedekind, J.E. / Reed, G.H. / Rayment, I. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ebh.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ebh.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 1ebh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/1ebh ftp://data.pdbj.org/pub/pdb/validation_reports/eb/1ebh | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO A 143 / 2: CIS PROLINE - PRO B 143 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.49366, -1.0E-5, -0.86965), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN B. THIS TRANSFORMATION IS A TWO-FOLD OPERATION AND TRANSLATION THAT DESCRIBE THE APPROXIMATE NON-CRYSTALLOGRAPHIC DYAD. THE CRYSTALLOGRAPHICALLY INDEPENDENT UNIT IS ONE DIMER OF CHEMICALLY IDENTICAL SUBUNITS. | |
-Components
#1: Protein | Mass: 46732.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00924, phosphopyruvate hydratase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THIS STRUCTURE COMPLEMENTS THE STUDY OF ENOLASE-BIS(MG)II-PHAH AND SERVES AS A CONTROL EXPERIMENT ...THIS STRUCTURE COMPLEMENT | Nonpolymer details | METALS ARE HEXACOORDINATE WITH OCTAHEDRAL GEOMETRY. A CHLORIDE ION IS BOUND AT THE PHOSPHATE ...METALS ARE HEXACOORDI | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.78 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Details: CRYSTALS WERE GROWN FROM POLYETHYLENE GLYCOL, KCL, AT PH 8.1. CRYSTALLIZED IN THE PRESENCE OF 0.5 MILLIMOLAR MG2+ | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 100 Å / Num. obs: 53410 / % possible obs: 75 % / Num. measured all: 77897 / Rmerge(I) obs: 0.041 |
---|---|
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2.02 Å / Num. unique obs: 6194 / Num. measured obs: 6392 / Rmerge(I) obs: 0.29 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→50 Å / σ(F): 0 Details: OCCUPANCIES FOR RESIDUES EXHIBITING DUAL CONFORMATIONS HAVE TOTAL OCCUPANCIES OF 1.0 WITH THE FOLLOWING EXCEPTION. ALA A 38 AND ALA B 38 WERE MODELED IN THE OPEN CONFORMATION ONL AFTER ATOM ...Details: OCCUPANCIES FOR RESIDUES EXHIBITING DUAL CONFORMATIONS HAVE TOTAL OCCUPANCIES OF 1.0 WITH THE FOLLOWING EXCEPTION. ALA A 38 AND ALA B 38 WERE MODELED IN THE OPEN CONFORMATION ONL AFTER ATOM N ALA 38 IN EACH CHAIN. THE TOTAL OCCUPANCIES FOR ATOMS OF THIS RESIDUE TOTAL 0.7.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|