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- PDB-4am3: Crystal structure of C. crescentus PNPase bound to RNA -

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Basic information

Entry
Database: PDB / ID: 4am3
TitleCrystal structure of C. crescentus PNPase bound to RNA
Components
  • POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASEPolynucleotide phosphorylase
  • RNA, 5'-R(*UP*AP*AP*CP*UP*UP*UP*GP*GP)-3'
KeywordsTRANSFERASE/RNA / TRANSFERASE-RNA COMPLEX / KH DOMAIN / RNASE E
Function / homology
Function and homology information


polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / mRNA catabolic process / RNA processing / magnesium ion binding / RNA binding / cytoplasm
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain / 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 ...Polyribonucleotide nucleotidyltransferase, RNA-binding domain / 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 / S1 domain profile. / Ribosomal Protein S5; domain 2 / 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 / RNA / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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
DepositionMar 7, 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
D: RNA, 5'-R(*UP*AP*AP*CP*UP*UP*UP*GP*GP)-3'
E: RNA, 5'-R(*UP*AP*AP*CP*UP*UP*UP*GP*GP)-3'
H: RNA, 5'-R(*UP*AP*AP*CP*UP*UP*UP*GP*GP)-3'
I: RNA, 5'-R(*UP*AP*AP*CP*UP*UP*UP*GP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,76113
Polymers242,1917
Non-polymers5706
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12620 Å2
ΔGint-88.7 kcal/mol
Surface area72740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.640, 112.060, 236.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 76952.133 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: RNA chain
RNA, 5'-R(*UP*AP*AP*CP*UP*UP*UP*GP*GP)-3' /


Mass: 2833.711 Da / Num. of mol.: 4 / Fragment: CO-PURIFIED RNA FROM E. COLI EXPRESSION STRAIN / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsADENOSINE-5'-MONOPHOSPHATE (A): H1 DISORDERED AND BASE ONLY IS MODELLED PHOSPHATE ION (PO4): TWO ...ADENOSINE-5'-MONOPHOSPHATE (A): H1 DISORDERED AND BASE ONLY IS MODELLED PHOSPHATE ION (PO4): TWO PHOSPHATES MOLECULES MODELLED AT EACH ACTIVE SITE URIDINE-5'-MONOPHOSPHATE (U): E7, D1, I1 DISORDERED AND BASE ONLY IS MODELLED
Sequence detailsN-TERMINAL GST TAG, GST TAG REMOVED.

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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: 2.58 Å3/Da / Density % sol: 52.39 % / Description: NONE
Crystal growDetails: 24% WT/V PEG 3350, 0.1 M BIS-TRIS PH 5.5, 0.1 M AMMONIUM ACETATE

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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 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. obs: 50090 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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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: 3→34.87 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.881 / SU B: 37.328 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RNA CHAIN E RESIDUE 7 IS DISORDERED AND BASE IS NOT MODELLED RNA CHAINS D I AND H ARE DISORDERED AND BASE ONLY IS MODELLED. S1 DOMAINS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RNA CHAIN E RESIDUE 7 IS DISORDERED AND BASE IS NOT MODELLED RNA CHAINS D I AND H ARE DISORDERED AND BASE ONLY IS MODELLED. S1 DOMAINS RESIDUES 623-712 WERE NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.25391 2539 5.1 %RANDOM
Rwork0.2099 ---
obs0.21216 47529 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 3→34.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13720 211 30 54 14015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914193
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.96619274
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97551861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66424.76542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.313152328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.541580
X-RAY DIFFRACTIONr_chiral_restr0.1240.22238
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110525
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→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 188 -
Rwork0.328 3210 -
obs--99.3 %
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)
14.4676-2.0557-1.8458.66373.49633.986-0.0316-0.05320.1063-0.3922-0.0383-0.544-0.1528-0.21590.06990.6183-0.0086-0.02160.09180.02850.2133-46.401354.5885-74.6216
24.1570.62381.13114.1348-3.3539.60210.06860.15780.4284-0.5563-0.33920.07151.03140.95150.27060.56690.09760.04570.23960.02140.0504-21.982836.246-79.1428
35.94190.80073.02353.88262.58745.73310.00480.03-0.1671-0.31060.0756-0.0265-0.02880.3218-0.08040.3197-0.04740.17120.44730.10220.1508-18.180963.4945-79.3499
40.9124-0.54080.39610.6039-0.06790.62850.0562-0.04480.14210.0374-0.00660.00690.4989-0.0103-0.04960.62680.0007-0.05320.2143-0.01860.2603-39.734527.761-36.2859
50.152-0.29740.16331.65390.01630.4380.0290.16690.16260.0735-0.1886-0.0470.0950.47920.15960.02840.0650.02440.77860.11450.3467-0.267456.9861-40.5016
60.36470.1658-0.05751.1529-0.11450.91930.00690.0249-0.0590.1181-0.10230.041-0.2767-0.09630.09540.43290.0246-0.03070.2912-0.0230.349-44.858576.5288-36.4699
70.08330.1561-0.19681.1062-0.14881.13330.034-0.0610.0547-0.0673-0.03560.14390.137-0.19280.00160.3019-0.0505-0.02490.4128-0.03010.3951-56.6547.2946-39.8728
80.92620.50960.31880.5505-0.30091.010.03980.1050.0937-0.1407-0.11520.00690.44080.40870.07540.40390.3230.03460.4816-0.03510.2377-9.609232.7353-44.0443
90.4963-0.11050.06930.406-0.11911.0126-0.02880.07280.02820.0321-0.1814-0.0602-0.21990.27250.21020.3349-0.1429-0.05080.3940.11270.3719-20.34981.2001-44.1694
105.2753-1.28812.18651.1893-1.87092.9526-0.3753-0.17280.63220.26890.029-0.1912-0.4046-0.04750.34630.77680.0822-0.00840.325-0.0810.1704-49.546944.356-5.1727
110.3283-1.1561-0.23987.00124.7495.3948-0.25790.37730.08741.3074-0.93610.65880.75020.30651.1940.4216-0.16830.05860.66810.14820.383-4.606239.0656-8.8134
122.05041.48-3.46941.3323-2.13496.39730.1502-0.5606-0.09730.3567-0.3701-0.04310.15561.02280.220.5617-0.0418-0.21520.5348-0.02210.2139-20.952582.5278-7.193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A556 - 619
2X-RAY DIFFRACTION2B556 - 619
3X-RAY DIFFRACTION3C556 - 619
4X-RAY DIFFRACTION4A1 - 230
5X-RAY DIFFRACTION5B1 - 230
6X-RAY DIFFRACTION6C1 - 230
7X-RAY DIFFRACTION7A331 - 553
8X-RAY DIFFRACTION8B331 - 553
9X-RAY DIFFRACTION9C331 - 553
10X-RAY DIFFRACTION10A233 - 310
11X-RAY DIFFRACTION11B233 - 310
12X-RAY DIFFRACTION12C233 - 310

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