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- PDB-1sn8: Crystal structure of the S1 domain of RNase E from E. coli (Pb de... -

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Basic information

Entry
Database: PDB / ID: 1sn8
TitleCrystal structure of the S1 domain of RNase E from E. coli (Pb derivative)
ComponentsRibonuclease E
KeywordsHYDROLASE / OB-fold / RNA-binding
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 / 7S RNA binding / RNA catabolic process / tRNA processing ...regulation of RNA helicase activity / rRNA 5'-end processing / ribonuclease E / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / protein homotetramerization / tRNA binding / molecular adaptor activity / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain ...Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
LEAD (II) ION / Ribonuclease E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsSchubert, M. / Edge, R.E. / Lario, P. / Cook, M.A. / Strynadka, N.C.J. / Mackie, G.A. / McIntosh, L.P.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural characterization of the RNase E S1 domain and identification of its oligonucleotide-binding and dimerization interfaces.
Authors: Schubert, M. / Edge, R.E. / Lario, P. / Cook, M.A. / Strynadka, N.C. / Mackie, G.A. / McIntosh, L.P.
History
DepositionMar 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _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_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.ptnr2_symmetry / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Ribonuclease E
B: Ribonuclease E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8234
Polymers21,4082
Non-polymers4142
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.580, 70.580, 87.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ribonuclease E / RNase E


Mass: 10704.134 Da / Num. of mol.: 2 / Fragment: S1 domain (residues 35-125)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RNE, AMS, HMP1, B1084 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P21513, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.6 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, sodium cacodylate, sodium acetate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.94739 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94739 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 15387 / Num. obs: 15387 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.925 % / Biso Wilson estimate: 22.98 Å2 / Rsym value: 0.091 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.338 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.841 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.16 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23223 783 5.1 %RANDOM
Rwork0.18229 ---
all0.18485 14555 --
obs0.18485 14555 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.749 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 2 229 1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211336
X-RAY DIFFRACTIONr_bond_other_d0.0020.021227
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9651801
X-RAY DIFFRACTIONr_angle_other_deg0.74632852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9455166
X-RAY DIFFRACTIONr_chiral_restr0.0830.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021500
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02273
X-RAY DIFFRACTIONr_nbd_refined0.2060.2211
X-RAY DIFFRACTIONr_nbd_other0.250.21384
X-RAY DIFFRACTIONr_nbtor_other0.0860.2843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.226
X-RAY DIFFRACTIONr_mcbond_it0.9461.5834
X-RAY DIFFRACTIONr_mcangle_it1.75221331
X-RAY DIFFRACTIONr_scbond_it2.5193502
X-RAY DIFFRACTIONr_scangle_it4.3154.5470
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.315 34
Rwork0.239 906

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