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- PDB-1iyx: Crystal structure of enolase from Enterococcus hirae -

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Basic information

Entry
Database: PDB / ID: 1iyx
TitleCrystal structure of enolase from Enterococcus hirae
ComponentsENOLASE
KeywordsLYASE / ENOLASE family
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / magnesium ion binding / cell surface / extracellular region
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
Biological speciesEnterococcus hirae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHosaka, T. / Meguro, T. / Yamato, I. / Shirakihara, Y.
CitationJournal: J.BIOCHEM.(TOKYO) / Year: 2003
Title: Crystal Structure of Enterococcus hirae Enolase at 2.8 A Resolution
Authors: Hosaka, T. / Meguro, T. / Yamato, I. / Shirakihara, Y.
History
DepositionSep 12, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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

Downloads & links

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Assembly

Deposited unit
A: ENOLASE
B: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,70612
Polymers92,9122
Non-polymers79310
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.510, 153.510, 90.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a dimer generated in the asymmetric unit by the operation: -x, -y, z

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Components

#1: Protein ENOLASE /


Mass: 46456.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterococcus hirae (bacteria) / References: UniProt: Q8GR70, phosphopyruvate hydratase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.84 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, lithium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris1reservoirpH7.5
225-30 %PEG40001reservoir
30.2 M1reservoirLi2SO4
45-8 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 25, 2001
RadiationMonochromator: rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 117740 / Num. obs: 30711 / % possible obs: 84.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.093
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EBH

1ebh


Resolution: 2.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 2554 RANDOM
Rwork0.175 --
obs0.246 25988 -
all-25999 -
Displacement parametersBiso mean: 39.0229 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 48 162 6718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005959
X-RAY DIFFRACTIONc_angle_deg1.21756
X-RAY DIFFRACTIONc_dihedral_angle_d22.28458
X-RAY DIFFRACTIONc_improper_angle_d0.76265
Refinement
*PLUS
Highest resolution: 2.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.28458
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76265

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