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- PDB-4aid: Crystal structure of C. crescentus PNPase bound to RNase E recogn... -

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Basic information

Entry
Database: PDB / ID: 4aid
TitleCrystal structure of C. crescentus PNPase bound to RNase E recognition peptide
Components
  • POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASEPolynucleotide phosphorylase
  • RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE 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 / tRNA binding / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain / : / 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 / : / 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 / 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
PHOSPHATE ION / Ribonuclease E / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHardwick, S.W. / Gubbey, T. / Hug, I. / Jenal, U. / Luisi, B.F.
CitationJournal: Open Biol. / Year: 2012
Title: Crystal Structure of Caulobacter Crescentus Polynucleotide Phosphorylase Reveals a Mechanism of RNA Substrate Channelling and RNA Degradosome Assembly.
Authors: Hardwick, S.W. / Gubbey, T. / Hug, I. / Jenal, U. / Luisi, B.F.
History
DepositionFeb 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Other
Revision 1.2Feb 5, 2014Group: Database references / Source and taxonomy
Revision 1.3Dec 20, 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 / struct_site
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 / _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
B: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
C: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
F: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
G: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
H: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1579
Polymers239,8726
Non-polymers2853
Water3,621201
1
A: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
F: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

A: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
F: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

A: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
F: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1579
Polymers239,8726
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area14140 Å2
ΔGint-84.4 kcal/mol
Surface area68950 Å2
MethodPISA
2
B: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
G: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

B: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
G: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

B: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
G: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1579
Polymers239,8726
Non-polymers2853
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area14310 Å2
ΔGint-71.3 kcal/mol
Surface area66640 Å2
MethodPISA
3
C: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
H: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

C: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
H: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

C: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
H: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1579
Polymers239,8726
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area13070 Å2
ΔGint-86.5 kcal/mol
Surface area61410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.439, 157.439, 302.379
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE / Polynucleotide phosphorylase / PNPASE / POLYNUCLEOTIDE PHOSPHORYLASE


Mass: 78159.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER VIBRIOIDES (bacteria) / Strain: CB15 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9AC32, polyribonucleotide nucleotidyltransferase
#2: Protein/peptide RIBONUCLEASE, RNE/RNG FAMILY PROTEIN / / RNASE E


Mass: 1798.081 Da / Num. of mol.: 3 / Fragment: PNPASE BINDING PEPTIDE - GWW, RESIDUES 885-898 / Source method: obtained synthetically / Source: (synth.) CAULOBACTER VIBRIOIDES (bacteria) / References: UniProt: Q9A749
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.01 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 19% WT/V PEG 3350, 0.15 M DL-MALIC ACID

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 85896 / % possible obs: 93.2 % / Observed criterion σ(I): 2.4 / Redundancy: 6.3 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 5.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GME

3gme


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.897 / SU B: 19.334 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.CHAIN C, RESIDUES 279-296 WERE DISORDERED AND WERE NOT MODELLED. NCS APPLIED AS AUTOMATICALLY GENERATED GLOBAL OPTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.25447 2322 3 %RANDOM
Rwork0.209 ---
obs0.21037 75066 89.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.002 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12436 0 15 201 12652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01912672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2651.97417189
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.93451684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27824.297491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.782152042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2891576
X-RAY DIFFRACTIONr_chiral_restr0.1440.21977
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219537
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 194 -
Rwork0.321 5615 -
obs--91.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.69470.271-0.06540.5326-0.08240.01590.0575-0.10570.0743-0.0091-0.05330.0713-0.01640.0299-0.00420.3302-0.00950.02080.3163-0.0010.1998-4.915725.2414-36.035
20.7061-0.28830.00670.5882-0.07140.01350.04440.0998-0.11810.0123-0.04190.09620.00540.0308-0.00260.33840.001-0.03830.30930.00410.1891-5.320665.4274-64.4244
32.0469-0.21380.10293.3556-0.69670.15830.00850.1899-0.1234-0.0751-0.00940.45560.01120.01680.00090.04470.02220.02270.1018-0.08350.777852.662646.5823-52.4007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 613
2X-RAY DIFFRACTION2B-1 - 556
3X-RAY DIFFRACTION3C-1 - 555

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