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- PDB-2po0: Crystal structure of the P. abyssi exosome RNase PH ring complexe... -

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Basic information

Entry
Database: PDB / ID: 2po0
TitleCrystal structure of the P. abyssi exosome RNase PH ring complexed with ADP in double conformation
Components
  • Probable exosome complex exonuclease 1
  • Probable exosome complex exonuclease 2
Keywordshydrolase/hydrolase / RNase PH / hydrolase-hydrolase COMPLEX
Function / homology
Function and homology information


exosome (RNase complex) / RNA catabolic process / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / cytoplasm
Similarity search - Function
Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / 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 ...Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / 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 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Exosome complex component Rrp42 / Exosome complex component Rrp41
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNavarro, M.V.A.S. / Guimaraes, B.G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Insights into the mechanism of progressive RNA degradation by the archaeal exosome.
Authors: Navarro, M.V.A.S. / Oliveira, C.C. / Zanchin, N.I. / Guimaraes, B.G.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7716
Polymers57,9892
Non-polymers7824
Water2,720151
1
A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules

A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules

A: Probable exosome complex exonuclease 1
B: Probable exosome complex exonuclease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,31318
Polymers173,9676
Non-polymers2,34512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area20750 Å2
ΔGint-166.4 kcal/mol
Surface area58700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.200, 94.200, 127.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsThe biological assembly is a hexamer generated from the heterodimer in the asymmetric unit by the operations: -y, x-y+1, z and -x+y-1, -x, z

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Components

#1: Protein Probable exosome complex exonuclease 1


Mass: 27720.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: Rrp41 / Plasmid: pET29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9V119, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein Probable exosome complex exonuclease 2


Mass: 30268.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: Rrp42 / Plasmid: pAE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9V118, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris, 45% MPD and 0.1 M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 2.3→44.23 Å / Num. all: 29661 / Num. obs: 28933 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.093 / Net I/σ(I): 16.5
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 4220 / Rsym value: 0.451 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PNZ

2pnz


Resolution: 2.3→19.98 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.416 / SU ML: 0.177 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.291 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24253 1433 5.1 %RANDOM
Rwork0.19019 ---
all0.19281 28026 --
obs0.19281 26541 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.197 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 54 175 4129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224036
X-RAY DIFFRACTIONr_angle_refined_deg2.1562.0215467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4775503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86124.848165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.14815751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7961528
X-RAY DIFFRACTIONr_chiral_restr0.130.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022929
X-RAY DIFFRACTIONr_nbd_refined0.2410.22005
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.218
X-RAY DIFFRACTIONr_mcbond_it0.7511.52591
X-RAY DIFFRACTIONr_mcangle_it1.14824066
X-RAY DIFFRACTIONr_scbond_it2.24431610
X-RAY DIFFRACTIONr_scangle_it3.2084.51401
LS refinement shellResolution: 2.3→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 84 -
Rwork0.251 1681 -
obs-1765 83.97 %
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)
12.37920.22320.81054.65520.42971.88550.0141-0.01110.00380.19810.0124-0.2067-0.01320.6162-0.0265-0.2750.0365-0.0220.03990.0085-0.0955-18.158423.935838.2209
21.7241-0.0803-0.14452.09991.03224.2702-0.02280.05320.0222-0.0560.0313-0.0706-0.45360.2831-0.0084-0.097-0.1484-0.0219-0.23320.03-0.1782-32.430351.321131.2015
30.7329-0.716-0.12411.64860.07710.92610.00680.0766-0.00730.0086-0.0126-0.1018-0.12540.34030.0058-0.1456-0.1369-0.0197-0.11550.0163-0.0618-27.217840.173932.6227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 2449 - 244
2X-RAY DIFFRACTION2BB8 - 27411 - 277
3X-RAY DIFFRACTION3A - BG - H301 - 3731 - 92

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