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- PDB-3gme: Crystal Structure of Polynucleotide Phosphorylase in complex with... -

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Basic information

Entry
Database: PDB / ID: 3gme
TitleCrystal Structure of Polynucleotide Phosphorylase in complex with RNase E and manganese
Components
  • Polyribonucleotide nucleotidyltransferasePolynucleotide phosphorylase
  • 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 / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing ...ribonuclease E / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / 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 / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, 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 / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / 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 / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Ribonuclease E / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesEscherichia coli E24377A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionMar 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1084
Polymers63,9982
Non-polymers1102
Water2,846158
1
A: Polyribonucleotide nucleotidyltransferase
D: Ribonuclease E
hetero molecules

A: Polyribonucleotide nucleotidyltransferase
D: Ribonuclease E
hetero molecules

A: Polyribonucleotide nucleotidyltransferase
D: Ribonuclease E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,32512
Polymers191,9956
Non-polymers3306
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15840 Å2
ΔGint-100 kcal/mol
Surface area59420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.574, 158.574, 156.118
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsOne RNase E recognition microdomain binds to one monomer of PNPase

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Components

#1: Protein Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / Polynucleotide phosphorylase / PNPase


Mass: 59657.812 Da / Num. of mol.: 1 / Fragment: Polynucleotide phosphorylase, 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.: 1
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
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growMethod: vapor diffusion
Details: 2.5 M NaCl, 9 % w/v PEG 6000, 20 mM Na- citrate, 20 mM manganese acetate , VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.4→25.91 Å / Num. all: 27941 / Num. obs: 27938 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.125
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.8 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25.91 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29758 1490 5.1 %RANDOM
Rwork0.28561 ---
obs0.28621 27938 99.34 %-
all-27941 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.586 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 2 158 3854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223757
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7651.9655103
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5755497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14424.702151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75215596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1381522
X-RAY DIFFRACTIONr_chiral_restr0.0450.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022838
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1360.21632
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2840.22565
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5331.52490
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.723980
X-RAY DIFFRACTIONr_scbond_it3.81931267
X-RAY DIFFRACTIONr_scangle_it5.984.51123
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 117 -
Rwork0.363 1976 -
obs--98.82 %

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