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- PDB-1e9i: Enolase from E.coli -

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Basic information

Entry
Database: PDB / ID: 1e9i
TitleEnolase from E.coli
ComponentsENOLASE
KeywordsLYASE / DEGRADOSOME
Function / homology
Function and homology information


bacterial degradosome / regulation of vacuole fusion, non-autophagic / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / cell surface ...bacterial degradosome / regulation of vacuole fusion, non-autophagic / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / identical protein binding / membrane / 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
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsKuhnel, K. / Carpousis, A.J. / Luisi, B.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of the Escherichia Coli RNA Degradosome Component Enolase
Authors: Kuhnel, K. / Luisi, B.
History
DepositionOct 17, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENOLASE
B: ENOLASE
C: ENOLASE
D: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,53210
Polymers182,3144
Non-polymers2186
Water9,116506
1
A: ENOLASE
B: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2064
Polymers91,1572
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ENOLASE
D: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3266
Polymers91,1572
Non-polymers1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.883, 150.006, 127.411
Angle α, β, γ (deg.)90.00, 109.18, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.95991, -0.06736, -0.2721), (-0.0688, -0.88439, 0.46166), (-0.27174, 0.46187, 0.8443)51.4048, -5.53899, 8.97248
2given(0.99381, 0.10356, 0.04022), (-0.09957, 0.66963, 0.73599), (0.04929, -0.73544, 0.67579)-11.8162, 42.34035, 29.33316
3given(-0.97178, -0.15224, -0.1802), (-0.14947, -0.19359, 0.96963), (-0.1825, 0.9692, 0.16537)38.67458, 40.00534, 43.63807

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Components

#1: Protein
ENOLASE / 2-PHOSPHOGLYCERATE DEHYDRATASE / 2-PHOSPHO-D-GLYCERATE HYDRO-LYASE


Mass: 45578.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: ENO / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08324, UniProt: P0A6P9*PLUS, phosphopyruvate hydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN THE RNA DEGRADOSOME, A MULTI-ENZYME COMPLEX IMPORTANT IN RNA PROCESSING AND MESSENGER ...INVOLVED IN THE RNA DEGRADOSOME, A MULTI-ENZYME COMPLEX IMPORTANT IN RNA PROCESSING AND MESSENGER RNA DEGRADATION.

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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: 2.65 Å3/Da / Density % sol: 53.1 %
Crystal growpH: 7 / Details: 20% PEG3350, 0.2M MG ACETATE, pH 7.00
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 mg/mlenolase1drop
210 %(w/v)PEG33501drop
3100 mMmagnesium acetate1drop
420 %PEG33501reservoir
5200 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.472
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.472 Å / Relative weight: 1
ReflectionResolution: 2.48→27.97 Å / Num. obs: 63664 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 33
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 4 % / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 10 / % possible all: 90
Reflection shell
*PLUS
% possible obs: 90 % / Num. unique obs: 6458

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EBG

1ebg


Resolution: 2.48→27.97 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 6458 10.1 %RANDOM
Rwork0.229 ---
obs0.229 63664 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.7544 Å2 / ksol: 0.325073 e/Å3
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.96 Å20 Å26.63 Å2
2--19.94 Å20 Å2
3----11.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-27 Å
Luzzati sigma a0.38 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.48→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12340 0 10 506 12856
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.251.5
X-RAY DIFFRACTIONc_mcangle_it4.262
X-RAY DIFFRACTIONc_scbond_it02
X-RAY DIFFRACTIONc_scangle_it02.5
LS refinement shellResolution: 2.47→2.56 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.318 466 9.4 %
Rwork0.26 4500 -
obs--72.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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