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- PDB-1nel: FLUORIDE INHIBITION OF YEAST ENOLASE: CRYSTAL STRUCTURE OF THE EN... -

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Entry
Database: PDB / ID: 1nel
TitleFLUORIDE INHIBITION OF YEAST ENOLASE: CRYSTAL STRUCTURE OF THE ENOLASE-MG2+-F--PI COMPLEX AT 2.6-ANGSTROMS RESOLUTION
ComponentsENOLASE
KeywordsCARBON-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
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLUORIDE ION / PHOSPHATE ION / Enolase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsLebioda, L. / Zhang, E. / Lewinski, K. / Brewer, M.J.
Citation
Journal: Proteins / Year: 1993
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: 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.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.
#5: 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.
#6: 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.
#7: 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
DepositionAug 20, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET 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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8294
Polymers46,6911
Non-polymers1383
Water4,936274
1
A: ENOLASE
hetero molecules

A: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6588
Polymers93,3812
Non-polymers2776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Unit cell
Length a, b, c (Å)122.500, 122.500, 67.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Atom site foot note1: 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 ENOLASE


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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ENO1_YEAST SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE LYS 84 SER 84

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 %protein1drop
22 mM1dropMg2+
31 mMEDTA1drop
41 mMdithiothreitol1drop
50.05 Mcitrate1drop
655 %satammonium sulfate1drop
755 %satammonium sulphate1reservoir

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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
Reflection shell
*PLUS
Highest resolution: 2.59 Å / Lowest resolution: 2.66 Å / % possible obs: 68 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2.6 Å / σ(F): 3 /
RfactorNum. reflection
obs0.169 15142
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 7 274 3570
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0470.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0530.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd0.250.45
X-RAY DIFFRACTIONp_multtor_nbd0.290.45
X-RAY DIFFRACTIONp_xhyhbond_nbd0.330.45
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.63
X-RAY DIFFRACTIONp_staggered_tor19.812
X-RAY DIFFRACTIONp_orthonormal_tor31.816
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: X-PLOR / Classification: refinement
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
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_planar_d
X-RAY DIFFRACTIONx_plane_restr
X-RAY DIFFRACTIONx_chiral_restr
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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