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

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Basic information

Entry
Database: PDB / ID: 4aim
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 / KH DOMAIN / S1 DOMAIN / GWW PEPTIDE
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
: / 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 / K Homology domain, type 1 / 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. / Ribosomal Protein S8; Chain: A, domain 1 / 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 / Nucleic acid-binding proteins / K Homology domain / K homology RNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / 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: 3.3 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 10, 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
C: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0383
Polymers79,9432
Non-polymers951
Water362
1
A: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
C: RIBONUCLEASE, RNE/RNG FAMILY PROTEIN
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)240,1159
Polymers239,8306
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 area14230 Å2
ΔGint-77.9 kcal/mol
Surface area86990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.329, 97.329, 191.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 78145.383 Da / Num. of mol.: 1
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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.28 Å3/Da / Density % sol: 62.52 % / Description: NONE
Crystal growDetails: 17 % WT/V PEG 3000, 0.1 M TRI-SODIUM CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Oct 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.3→40 Å / Num. obs: 15391 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.8
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 99.2

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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
Resolution: 3.3→38.73 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 25.049 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.51 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26026 771 5 %RANDOM
Rwork0.18553 ---
obs0.18927 14616 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.546 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 3.3→38.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 5 2 4957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195038
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9636874
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0955704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98224.611180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.75515701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2211524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213850
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: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 64 -
Rwork0.208 1038 -
obs--99.01 %
Refinement TLS params.Method: refined / Origin x: -37.4778 Å / Origin y: -6.7915 Å / Origin z: 100.042 Å
111213212223313233
T0.1232 Å20.0126 Å2-0.0258 Å2-0.7689 Å2-0.252 Å2--0.2034 Å2
L9.0218 °27.512 °2-4.7778 °2-21.9036 °2-14.1048 °2--9.0839 °2
S1.0108 Å °-0.041 Å °-0.3593 Å °1.1125 Å °-0.3024 Å °1.063 Å °-0.711 Å °0.1594 Å °-0.7085 Å °

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