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

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Basic information

Entry
Database: PDB / ID: 2pnz
TitleCrystal structure of the P. abyssi exosome RNase PH ring complexed with UDP and GMP
Components(Probable exosome complex exonuclease ...) x 2
Keywordshydrolase/hydrolase / RNase PH / hydrolase-hydrolase COMPLEX
Function / homology
Function and homology information


cytoplasmic exosome (RNase complex) / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / gene expression / RNA binding
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
GUANOSINE-5'-MONOPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Exosome complex component Rrp42 / Exosome complex component Rrp41
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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

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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)59,3479
Polymers57,9892
Non-polymers1,3587
Water4,306239
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)178,04227
Polymers173,9676
Non-polymers4,07521
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 area23400 Å2
ΔGint-237.4 kcal/mol
Surface area57870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.810, 93.810, 126.260
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

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Probable exosome complex exonuclease ... , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 246 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


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


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
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: Apr 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: 2.14→43.98 Å / Num. all: 36300 / Num. obs: 36060 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.8 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.172 / Net I/σ(I): 11.3
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 5542 / Rsym value: 0.639 / % 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 2BA0

2ba0


Resolution: 2.14→19.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.558 / SU ML: 0.157 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.205 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25481 1783 5 %RANDOM
Rwork0.18752 ---
all0.19088 34174 --
obs0.19088 33921 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.856 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.14→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 49 279 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224061
X-RAY DIFFRACTIONr_angle_refined_deg2.3122.0235507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8365511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.19624.848165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.36915757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2321528
X-RAY DIFFRACTIONr_chiral_restr0.1640.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022940
X-RAY DIFFRACTIONr_nbd_refined0.2430.22348
X-RAY DIFFRACTIONr_nbtor_refined0.3230.22789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2323
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.224
X-RAY DIFFRACTIONr_mcbond_it1.0371.52593
X-RAY DIFFRACTIONr_mcangle_it1.59324087
X-RAY DIFFRACTIONr_scbond_it2.78731626
X-RAY DIFFRACTIONr_scangle_it4.0744.51415
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 115 -
Rwork0.244 2290 -
obs-2405 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)
12.7310.3736-0.00111.78150.30091.4795-0.0020.0771-0.1777-0.03660.0344-0.09290.3460.1191-0.0324-0.06380.0860.0197-0.1409-0.01390.0009-30.05763.3672-37.7559
21.91230.09480.48141.73330.14492.75220.0174-0.1352-0.06690.1254-0.0330.00080.278-0.10170.0156-0.0957-0.07470.0204-0.1730.0128-0.1558-60.71872.8566-30.7068
31.6032-0.0042-0.14170.35150.01630.5715-0.0455-0.0457-0.0595-0.01480.0213-0.06150.2363-0.00120.02420.0095-0.0102-0.0023-0.15590.0070.0152-48.05552.6847-33.913
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 - BJ - K283 - 4201 - 139

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