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- PDB-2al2: Crystal Structure Analysis of Enolase Mg Subunit Complex at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 2al2
TitleCrystal Structure Analysis of Enolase Mg Subunit Complex at pH 8.0
Components(enolase 1) x 2
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 / 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
2-PHOSPHOGLYCERIC ACID / : / PHOSPHOENOLPYRUVATE / Enolase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSims, P.A. / Menefee, A.L. / Larsen, T.M. / Mansoorabadi, S.O. / Reed, G.H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure and catalytic properties of an engineered heterodimer of enolase composed of one active and one inactive subunit
Authors: Sims, P.A. / Menefee, A.L. / Larsen, T.M. / Mansoorabadi, S.O. / Reed, G.H.
History
DepositionAug 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,28912
Polymers93,4092
Non-polymers88010
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-67 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.700, 65.600, 85.900
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein enolase 1 / E.C.4.2.1.11 / 2-phosphoglycerate dehydratase / 2-phospho-D- glycerate hydro-lyase


Mass: 46674.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: active form
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ENO1, ENOA, HSP48 / Plasmid: PetEnol / Production host: Escherichia coli (E. coli) / References: UniProt: P00924, phosphopyruvate hydratase
#2: Protein enolase 1 / E.C.4.2.1.11 / 2-phosphoglycerate dehydratase / 2-phospho-D- glycerate hydro-lyase


Mass: 46734.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: inactive form
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ENO1, ENOA, HSP48 / Plasmid: PetEnol / Production host: Escherichia coli (E. coli) / References: UniProt: P00924, phosphopyruvate hydratase

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Non-polymers , 6 types, 545 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


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


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: batch / pH: 8
Details: PEG 8000, potasssium chloride, pH 8.0, Batch, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: BRUKER / Detector: CCD / Date: Apr 4, 2005
RadiationMonochromator: Pt-135 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→26 Å / Num. all: 67650 / Num. obs: 67650 / % possible obs: 100 %

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Processing

Software
NameClassification
SAINTdata scaling
SADABSdata reduction
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→26 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 3378 RANDOM
Rwork0.196 --
all0.1961 67650 -
obs0.1961 67650 -
Refinement stepCycle: LAST / Resolution: 1.85→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6545 0 48 535 7128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0056
X-RAY DIFFRACTIONs_angle_d1.24

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