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- PDB-2fym: Crystal structure of E. coli enolase complexed with the minimal b... -

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Basic information

Entry
Database: PDB / ID: 2fym
TitleCrystal structure of E. coli enolase complexed with the minimal binding segment of RNase E.
Components
  • Enolase
  • Ribonuclease E
KeywordsLYASE / RNA degradosome / enolase / RNase E
Function / homology
Function and homology information


regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity ...regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / 7S RNA binding / RNA catabolic process / tRNA processing / protein complex oligomerization / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / glycolytic process / cytoplasmic side of plasma membrane / rRNA processing / molecular adaptor activity / protein homotetramerization / tRNA binding / cytoskeleton / rRNA binding / magnesium ion binding / cell surface / protein homodimerization activity / RNA binding / zinc ion binding / extracellular region / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / Ribonuclease E / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E/G family / Enolase / Enolase, conserved site ...Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / Ribonuclease E / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E/G family / 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 / S1 domain profile. / Enolase-like; domain 1 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Enolase / Ribonuclease E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChandran, V. / Luisi, B.F.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Recognition of Enolase in the Escherichia coli RNA Degradosome
Authors: Chandran, V. / Luisi, B.F.
History
DepositionFeb 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Ribonuclease E
C: Enolase
D: Enolase
E: Ribonuclease E
F: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,50310
Polymers186,4056
Non-polymers974
Water34,7691930
1
A: Enolase
B: Ribonuclease E
C: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2515
Polymers93,2033
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-37 kcal/mol
Surface area27930 Å2
MethodPISA
2
D: Enolase
E: Ribonuclease E
F: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2515
Polymers93,2033
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-34 kcal/mol
Surface area27810 Å2
MethodPISA
3
A: Enolase
B: Ribonuclease E
C: Enolase
hetero molecules

D: Enolase
E: Ribonuclease E
F: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,50310
Polymers186,4056
Non-polymers974
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area12690 Å2
ΔGint-78 kcal/mol
Surface area53940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.054, 124.201, 96.076
Angle α, β, γ (deg.)90.00, 90.58, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit consists of a enolase dimer bound to a single RNase E peptide. Two biological units are present in a single asymmetric unit.

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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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6P9, phosphopyruvate hydratase
#2: Protein/peptide Ribonuclease E / RNase E


Mass: 2045.408 Da / Num. of mol.: 2 / Fragment: Residues 833-850 / Source method: obtained synthetically / Details: The E. coli RNase E peptide was synthesized.
References: UniProt: P21513, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1930 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4750.11
2
3
4
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop72.4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
2982vapor diffusion, hanging drop8.240% MPEG 550, 0.1M HEPES, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
2983vapor diffusion, hanging drop68% PEG 4K, 0.2 M imidazole maleate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
2984vapor diffusion, hanging drop7.527% PEG 600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF ID14-411
SYNCHROTRONESRF ID2920.9782
ROTATING ANODERIGAKU31.54
SYNCHROTRONESRF ID14-441
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 8, 2004
ADSC QUANTUM 2102CCDFeb 24, 2004
RIGAKU RAXIS IV3IMAGE PLATEMar 9, 2004
ADSC QUANTUM 44CCDMay 8, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ge(220) crystalSINGLE WAVELENGTHMx-ray1
2Si(111) crystalSINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
4Ge(220) crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97821
31.541
ReflectionResolution: 1.6→20 Å / Num. all: 216453 / Num. obs: 216432 / % possible obs: 91.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 13.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 16.51 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 2.45 / % possible all: 94.3

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Phasing

Phasing MRRfactor: 0.493 / Cor.coef. Fo:Fc: 0.724
Highest resolutionLowest resolution
Rotation1.6 Å19.99 Å
Translation1.6 Å19.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Enolase structure 1E9I

1e9i


Resolution: 1.6→19.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.234 / SU ML: 0.052 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20102 10847 5 %RANDOM
Rwork0.16472 ---
obs0.16652 205585 90.92 %-
all-216453 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12873 0 4 1930 14807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02213050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.96917604
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41351744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.26725.745517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.064152277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6741546
X-RAY DIFFRACTIONr_chiral_restr0.0830.22013
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029690
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.27024
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.29218
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.21764
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.278
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8441.58843
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.237213607
X-RAY DIFFRACTIONr_scbond_it2.69734702
X-RAY DIFFRACTIONr_scangle_it3.0784.53994
X-RAY DIFFRACTIONr_rigid_bond_restr2.495313545
X-RAY DIFFRACTIONr_sphericity_free3.55631934
X-RAY DIFFRACTIONr_sphericity_bonded2.843312873
LS refinement shellResolution: 1.598→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 820 -
Rwork0.201 15113 -
obs--91.22 %

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