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- PDB-1l8p: Mg-phosphonoacetohydroxamate complex of S39A yeast enolase 1 -

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Basic information

Entry
Database: PDB / ID: 1l8p
TitleMg-phosphonoacetohydroxamate complex of S39A yeast enolase 1
Componentsenolase 1
KeywordsLYASE / Beta Barrel
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 / 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
PHOSPHONOACETOHYDROXAMIC ACID / Enolase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPoyner, R.R. / Larsen, T.M. / Wong, S.W. / Reed, G.H.
CitationJournal: Arch.Biochem.Biophys. / Year: 2002
Title: Functional and structural changes due to a serine to alanine mutation in the active-site flap of enolase.
Authors: Poyner, R.R. / Larsen, T.M. / Wong, S.W. / Reed, G.H.
History
DepositionMar 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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.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.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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: enolase 1
B: enolase 1
C: enolase 1
D: enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,68216
Polymers186,8674
Non-polymers81512
Water25,7971432
1
A: enolase 1
B: enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8418
Polymers93,4342
Non-polymers4076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-54 kcal/mol
Surface area28970 Å2
MethodPISA
2
C: enolase 1
D: enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8418
Polymers93,4342
Non-polymers4076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-53 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.200, 164.100, 84.600
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
enolase 1 / 2-phosphoglycerate dehydratase / 2-phospho-D-glycerate hydro-lyase


Mass: 46716.797 Da / Num. of mol.: 4 / Mutation: S39A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: eno1 / Plasmid: pET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00924, phosphopyruvate hydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PAH / PHOSPHONOACETOHYDROXAMIC ACID


Mass: 155.047 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6NO5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1432 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 8000, Potassium Chloride, HEPPs, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Method: batch method / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
114 mg/mlprotein11
20.26 M11KCl
35 mM11MgCl2
44 mMPhAH11
550 mMHEPPS-KOH11pH8.0

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 13, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 97095 / Num. obs: 97095 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.031
Reflection shellResolution: 2.1→2.17 Å / % possible all: 96.8
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. measured all: 266980 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 96.2 % / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 91934 -RANDOM
Rwork0.1808 ---
all-96792 --
obs-96792 96.7 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13160 0 44 1432 14636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.2
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.181 / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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