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- PDB-1one: YEAST ENOLASE COMPLEXED WITH AN EQUILIBRIUM MIXTURE OF 2'-PHOSPHO... -

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Basic information

Entry
Database: PDB / ID: 1one
TitleYEAST ENOLASE COMPLEXED WITH AN EQUILIBRIUM MIXTURE OF 2'-PHOSPHOGLYCEATE AND PHOSPHOENOLPYRUVATE
ComponentsENOLASE
KeywordsLYASE / GLYCOLYSIS
Function / homology
Function and homology information


regulation of vacuole fusion, non-autophagic / Gluconeogenesis / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding ...regulation of vacuole fusion, non-autophagic / Gluconeogenesis / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding / mitochondrion / plasma membrane / cytosol / cytoplasm
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
2-PHOSPHOGLYCERIC ACID / PHOSPHOENOLPYRUVATE / Enolase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLarsen, T.M. / Wedekind, J.E. / Rayment, I. / Reed, G.H.
CitationJournal: Biochemistry / Year: 1996
Title: A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and ...Title: A carboxylate oxygen of the substrate bridges the magnesium ions at the active site of enolase: structure of the yeast enzyme complexed with the equilibrium mixture of 2-phosphoglycerate and phosphoenolpyruvate at 1.8 A resolution.
Authors: Larsen, T.M. / Wedekind, J.E. / Rayment, I. / Reed, G.H.
History
DepositionDec 5, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENOLASE
B: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,27110
Polymers93,4662
Non-polymers8058
Water16,970942
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-71 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.900, 73.200, 93.900
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ENOLASE / / 2-PHOSPHO-D-GLYCERATE HYDROLASE


Mass: 46732.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00924, phosphopyruvate hydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID / 2-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 942 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8 / Method: batch method / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlenolase11
215 %PEG800011
30.25 M11KCl
450 mMHEPPS/KOH11
52 mMP-enolpyruvate11
62 mM11MgCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 71494
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / % possible obs: 92 % / Num. measured all: 113340 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / % possible obs: 81 % / Num. possible: 6132 / Rmerge(I) obs: 0.132

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.8→60 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.177 --
obs-113340 92 %
Refinement stepCycle: LAST / Resolution: 1.8→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 46 942 7572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.1
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.009
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Rfactor all: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.009

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