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- PDB-7dol: Mycoplasma genitalium RNase R in complex with double-stranded RNA -

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Basic information

Entry
Database: PDB / ID: 7dol
TitleMycoplasma genitalium RNase R in complex with double-stranded RNA
Components
  • RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • Ribonuclease R
KeywordsHYDROLASE/RNA / RNA hydrolase / RNA 2'-O-methylation sensitive / HYDROLASE / HYDROLASE-RNA complex
Function / homology
Function and homology information


exoribonuclease II activity / exoribonuclease II / mRNA catabolic process / RNA binding / cytosol
Similarity search - Function
Ribonuclease R / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / Cold shock domain / Cold shock protein domain ...Ribonuclease R / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / Cold shock domain / Cold shock protein domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / Ribonuclease R
Similarity search - Component
Biological speciesMycoplasma genitalium G37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsAbula, A. / Quan, X. / Li, X. / Yang, T. / Li, T. / Chen, Q. / Ji, X.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.
Authors: Abula, A. / Li, X. / Quan, X. / Yang, T. / Liu, Y. / Guo, H. / Li, T. / Ji, X.
History
DepositionDec 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease R
C: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5503
Polymers87,5262
Non-polymers241
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-22 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.414, 96.085, 117.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease R / RNase R / VacB protein homolog


Mass: 85595.555 Da / Num. of mol.: 1 / Mutation: D284A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Strain: G-37 / Gene: rnr, vacB, MG104 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P47350, exoribonuclease II
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycoplasma genitalium G37 (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 295 K / Method: microbatch / Details: 100 mM CHES (pH9.5), 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 57987 / % possible obs: 99.9 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 1.087 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2865

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Processing

Software
NameVersionClassification
PHENIX1.10_2148refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XGU

5xgu


Resolution: 2.002→38.294 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 2000 3.45 %
Rwork0.2203 55901 -
obs0.221 57901 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.67 Å2 / Biso mean: 64.0564 Å2 / Biso min: 25.84 Å2
Refinement stepCycle: final / Resolution: 2.002→38.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 132 1 235 4914
Biso mean--25.84 59.44 -
Num. residues----571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084778
X-RAY DIFFRACTIONf_angle_d1.1566511
X-RAY DIFFRACTIONf_chiral_restr0.066767
X-RAY DIFFRACTIONf_plane_restr0.005809
X-RAY DIFFRACTIONf_dihedral_angle_d16.3942880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0023-2.05240.35051390.3032387599
2.0524-2.10780.32761410.30963948100
2.1078-2.16990.29381410.25743945100
2.1699-2.23990.27361410.25163941100
2.2399-2.31990.31071420.26313965100
2.3199-2.41280.25261420.24483960100
2.4128-2.52260.27361430.23433981100
2.5226-2.65560.24381410.23183965100
2.6556-2.82190.29781420.23433976100
2.8219-3.03970.23821440.24024009100
3.0397-3.34540.22841430.21964009100
3.3454-3.82910.21781440.20364043100
3.8291-4.82280.20861460.18574064100
4.8228-38.20060.23951510.2168422099
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)
10.11160.158-0.02570.2311-0.19630.1452-0.0954-0.8256-0.21330.9023-0.0702-0.34260.18020.1102-0.00161.1542-0.0950.03680.74030.04260.6489-1.3302-15.743653.91
20.9675-0.14480.34021.25210.34430.6359-0.0019-0.34620.26790.25340.0898-0.1226-0.29190.29660.00240.4476-0.0569-0.03320.4773-0.08560.468612.1334-8.890936.5925
32.12730.3326-0.17291.02040.33992.29770.03930.09660.2514-0.11670.0255-0.071-0.36280.1504-00.3449-0.02760.02730.2735-0.03260.3349.4463-13.01789.3833
41.2230.3786-0.06980.17580.25791.09790.1251-0.10230.0276-0.0555-0.0866-0.0185-0.0832-0.0755-0.00030.35510.01090.02680.3375-0.02370.3035-0.9054-17.986417.1512
50.23740.53350.23412.93810.63431.50350.1841-0.39210.1024-0.0281-0.23940.54330.1965-0.1324-0.05220.2929-0.034-0.02560.2941-0.01580.3847-3.9086-28.598818.7604
60.7947-0.1618-0.79020.72370.34330.692-0.2177-0.765-0.52940.32840.10370.43280.11270.28150.02570.3620.0045-0.04190.3874-0.06610.38095.3296-19.729930.9517
72.0216-0.1237-0.74530.5178-0.21341.32330.405-0.0010.40460.4359-0.6460.31940.6867-2.38960.06540.6715-0.24650.06030.9796-0.32050.6402-21.9363-8.174333.9747
8-0.0090.0064-0.06830.0416-0.06360.05980.2631-0.69380.42940.2319-0.18550.6359-0.36540.2280.00030.5297-0.00550.03470.5078-0.0680.6159-1.5973-17.745919.7466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 85 through 185 )A85 - 185
2X-RAY DIFFRACTION2chain 'A' and (resid 186 through 272 )A186 - 272
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 427 )A273 - 427
4X-RAY DIFFRACTION4chain 'A' and (resid 428 through 493 )A428 - 493
5X-RAY DIFFRACTION5chain 'A' and (resid 494 through 598 )A494 - 598
6X-RAY DIFFRACTION6chain 'A' and (resid 599 through 641 )A599 - 641
7X-RAY DIFFRACTION7chain 'A' and (resid 642 through 725 )A642 - 725
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 9 )C4 - 9

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