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- PDB-3gcm: Crystal Structure of E. coli polynucleotide phosphorylase bound t... -

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Basic information

Entry
Database: PDB / ID: 3gcm
TitleCrystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E
Components
  • Polyribonucleotide nucleotidyltransferase
  • Ribonuclease E
Keywordstransferase / protein binding / Protein-RNA complex / Cytoplasm / Nucleotidyltransferase / RNA-binding / Transferase / Hydrolase / transferase - protein binding COMPLEX
Function / homology
Function and homology information


ribonuclease E / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing ...ribonuclease E / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain / 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 / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily ...Polyribonucleotide nucleotidyltransferase, RNA-binding domain / 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 / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K Homology domain / K homology RNA-binding domain / Arc Repressor Mutant, subunit A / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / CITRATE ANION / Ribonuclease E / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesEscherichia coli E24377A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNurmohamed, S. / Luisi, B.L.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.
Authors: Nurmohamed, S. / Vaidialingam, B. / Callaghan, A.J. / Luisi, B.F.
History
DepositionFeb 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Polyribonucleotide nucleotidyltransferase
D: Ribonuclease E
B: Polyribonucleotide nucleotidyltransferase
E: Ribonuclease E
C: Polyribonucleotide nucleotidyltransferase
F: Ribonuclease E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,67120
Polymers191,9956
Non-polymers2,67514
Water15,925884
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23000 Å2
ΔGint-80 kcal/mol
Surface area62910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.335, 176.335, 189.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDEF

#1: Protein Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / PNPase


Mass: 59657.812 Da / Num. of mol.: 3 / Fragment: residues 1-549 / Source method: isolated from a natural source / Source: (natural) Escherichia coli E24377A (bacteria) / Strain: BL21 DE3
References: UniProt: A7ZS61, polyribonucleotide nucleotidyltransferase
#2: Protein/peptide Ribonuclease E


Mass: 4340.687 Da / Num. of mol.: 3
Fragment: RNase E recognition microdomain, residues 1021-1061
Source method: obtained synthetically / Details: This sequence occurs naturally in E. coli
References: UniProt: A7ZKI9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 4 types, 898 molecules

#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / 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: 3.84 Å3/Da / Density % sol: 67.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M ammonium hydrogen citrate, 17 % w/v PEG 3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2006 / Details: Monochromator
RadiationMonochromator: horizontally diffracting silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 102846 / Num. obs: 97645 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 27.176 Å2
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3H

1e3h


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.883 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22065 5134 5 %RANDOM
Rwork0.16639 ---
all0.201 102846 --
obs0.16911 97645 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.176 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12865 0 167 884 13916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02213247
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.98117995
X-RAY DIFFRACTIONr_angle_other_deg1.247322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73551709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49524.429578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.951152217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.70315101
X-RAY DIFFRACTIONr_chiral_restr0.1520.22073
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210052
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.25679
X-RAY DIFFRACTIONr_nbd_other0.140.217
X-RAY DIFFRACTIONr_nbtor_refined0.3090.29038
X-RAY DIFFRACTIONr_nbtor_other0.0510.27
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2716
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2291.58728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01213614
X-RAY DIFFRACTIONr_scbond_it3.36135073
X-RAY DIFFRACTIONr_scangle_it5.444.54369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 369 -
Rwork0.244 7130 -
obs--99.63 %

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