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- PDB-2po2: Crystal structure of the P. abyssi exosome RNase PH ring complexe... -

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Basic information

Entry
Database: PDB / ID: 2po2
TitleCrystal structure of the P. abyssi exosome RNase PH ring complexed with CDP
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 / 3' exoribonuclease family, domain 1 / Ribosomal Protein S5; domain 2 ...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
CYTIDINE-5'-DIPHOSPHATE / Exosome complex component Rrp42 / Exosome complex component Rrp41
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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)58,9838
Polymers57,9892
Non-polymers9946
Water3,171176
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)176,95024
Polymers173,9676
Non-polymers2,98218
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 area21990 Å2
ΔGint-229.8 kcal/mol
Surface area57630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.498, 93.498, 125.714
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-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


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


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.23 %
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 20, 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: 2.4→43.63 Å / Num. all: 25254 / Num. obs: 25053 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 40.3 Å2 / Rsym value: 0.124 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 4012 / Rsym value: 0.607 / % possible all: 96

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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: 2.41→19.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.254 / SU ML: 0.19 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.341 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25852 1273 5.1 %RANDOM
Rwork0.18233 ---
all0.18603 23886 --
obs0.18603 23727 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.41→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 25 216 4144
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.021
X-RAY DIFFRACTIONr_angle_refined_deg2.106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.579
X-RAY DIFFRACTIONr_chiral_restr0.127
X-RAY DIFFRACTIONr_gen_planes_refined0.007
X-RAY DIFFRACTIONr_nbd_refined0.242
X-RAY DIFFRACTIONr_nbtor_refined0.324
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.192
LS refinement shellResolution: 2.41→2.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 91 -
Rwork0.23 1590 -
obs-1681 92.82 %
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)
13.94180.14680.12621.96550.61652.2832-0.00770.0389-0.25430.01450.0462-0.08460.48730.2536-0.0385-0.0910.10360.0241-0.1996-0.0044-0.0389-29.89983.4298-37.5581
22.56370.07460.87191.88930.00843.68050.0392-0.13-0.13720.1771-0.06090.02510.3734-0.16160.0217-0.1097-0.08310.035-0.21330.0212-0.1529-60.54092.5841-30.6802
32.004-0.0219-0.08050.52230.07860.4518-0.0557-0.0688-0.0256-0.00450.0518-0.04940.2498-0.03810.0039-0.0381-0.021-0.0058-0.16520.0211-0.0797-47.61924.6663-33.8176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA - C9 - 2509 - 1
2X-RAY DIFFRACTION2BB - J8 - 28311 - 1
3X-RAY DIFFRACTION3A - BI - J284 - 3821 - 100

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