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- PDB-2wnr: The structure of Methanothermobacter thermautotrophicus exosome c... -

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Basic information

Entry
Database: PDB / ID: 2wnr
TitleThe structure of Methanothermobacter thermautotrophicus exosome core assembly
Components
  • PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
  • PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
KeywordsHYDROLASE / PHOSPHATE BINDING / 3'-5' EXORIBONUCLEASE / EXOSOME / NUCLEASE / EXONUCLEASE
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
PHOSPHATE ION / Exosome complex component Rrp42 / Exosome complex component Rrp41
Similarity search - Component
Biological speciesMETHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsNg, C.L. / Waterman, D.G. / Antson, A.A. / Ortiz-Lombardia, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of the Methanothermobacter Thermautotrophicus Exosome Rnase Ph Ring
Authors: Ng, C.L. / Waterman, D.G. / Antson, A.A. / Ortiz-Lombardia, M.
History
DepositionJul 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 30, 2012Group: Other
Revision 1.3Dec 13, 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
Remark 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ... THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
B: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
C: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
D: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
E: PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
F: PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,7409
Polymers169,4556
Non-polymers2853
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16050 Å2
ΔGint-84.3 kcal/mol
Surface area55760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.261, 118.233, 154.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12B
22D
32F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A37 - 68
2111C37 - 68
3111E37 - 68
1211A80 - 125
2211C80 - 125
3211E80 - 125
1311A133 - 172
2311C133 - 172
3311E133 - 172
1411A194 - 250
2411C194 - 250
3411E194 - 250
1511A266 - 272
2511C266 - 272
3511E266 - 272
1121B33 - 63
2121D33 - 63
3121F33 - 63
1221B78 - 94
2221D78 - 94
3221F78 - 94
1321B97 - 115
2321D97 - 115
3321F97 - 115
1421B125 - 169
2421D125 - 169
3421F125 - 169
1521B189 - 194
2521D189 - 194
3521F189 - 194
1621B199 - 213
2621D199 - 213
3621F199 - 213
1721B217 - 233
2721D217 - 233
3721F217 - 233

NCS ensembles :
ID
1
2

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Components

#1: Protein PROBABLE EXOSOME COMPLEX EXONUCLEASE 2


Mass: 29924.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Strain: DELTA H / Plasmid: PCDFDUET, PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566
References: UniProt: O26778, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein PROBABLE EXOSOME COMPLEX EXONUCLEASE 1


Mass: 26560.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOTHERMOBACTER THERMAUTOTROPHICUS (archaea)
Strain: DELTA H / Plasmid: PCDFDUET, PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566
References: UniProt: O26779, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.45 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 7
Details: 20% PEG3350, 0.1M SUCCINIC ACID PH 7.0, 5% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9191
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 2.65→25 Å / Num. obs: 47654 / % possible obs: 98.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.5 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR2

2br2


Resolution: 2.65→24.86 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / SU B: 31.794 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.231 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25077 973 2 %RANDOM
Rwork0.21137 ---
obs0.21218 46606 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.65→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10910 0 15 125 11050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2572.00214976
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60251414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77824.112484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.141152053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.70515111
X-RAY DIFFRACTIONr_chiral_restr0.0880.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218215
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_it1.0331.57071
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.817211455
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1134009
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6374.53519
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1350tight positional0.050.05
12C1350tight positional0.040.05
13E1350tight positional0.040.05
21B1104tight positional0.050.05
22D1104tight positional0.050.05
23F1104tight positional0.050.05
11A1350tight thermal0.070.5
12C1350tight thermal0.070.5
13E1350tight thermal0.080.5
21B1104tight thermal0.080.5
22D1104tight thermal0.070.5
23F1104tight thermal0.080.5
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 70 -
Rwork0.29 3011 -
obs--88.36 %
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)
12.662-0.28590.07741.73160.76164.6621-0.0541-0.2835-0.23020.02010.07940.18630.1025-1.0044-0.02530.26920.0219-0.03770.28070.07740.3541-60.6032.51613.258
24.64850.4394-0.34221.2158-0.08454.04610.0243-0.3625-0.05710.00050.14380.06210.044-0.111-0.16820.30410.0581-0.07130.07380.02960.2181-37.4032.08525.788
34.2664-0.6567-0.03142.0841-0.61383.72480.23150.9056-0.0941-0.2495-0.08220.0213-0.1502-0.571-0.14930.33710.1097-0.02390.2832-0.01330.1984-41.0348.127-31.079
43.6895-0.7896-1.09041.4419-0.18015.89830.2030.56770.1587-0.04750.03140.1068-0.4984-1.1426-0.23440.34960.2963-0.01860.48410.12520.3103-62.19816.239-16.194
53.63780.2675-1.18441.48330.0413.8108-0.1362-0.2671-0.41010.07260.1129-0.14120.55740.78690.02330.40210.2004-0.09220.1908-0.02260.3131-13.887-7.3565.786
63.7713-1.14630.27321.2458-0.90834.37150.05230.03190.0892-0.05280.0618-0.1148-0.10.621-0.11410.2791-0.0325-0.00330.1415-0.08870.2774-11.3756.203-17.744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 269
2X-RAY DIFFRACTION2B15 - 236
3X-RAY DIFFRACTION3C13 - 270
4X-RAY DIFFRACTION4D16 - 236
5X-RAY DIFFRACTION5E21 - 270
6X-RAY DIFFRACTION6F14 - 237

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