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- PDB-7dic: Mycoplasma genitalium RNase R in complex with single-stranded RNA -

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Basic information

Entry
Database: PDB / ID: 7dic
TitleMycoplasma genitalium RNase R in complex with single-stranded RNA
Components
  • RNA (5'-R(P*AP*AP*AP*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: 2.242 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
DepositionNov 18, 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*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5383
Polymers88,5132
Non-polymers241
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-23 kcal/mol
Surface area30680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.258, 68.258, 354.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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*AP*AP*AP*A)-3')


Mass: 2917.895 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.: 128 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 295 K / Method: microbatch / Details: 100 mM KCl, 100 mM HEPES (pH 6.8), 15% PEG 5000MME

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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: 2.24→50 Å / Num. obs: 41557 / % possible obs: 99.4 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 18
Reflection shellResolution: 2.24→2.28 Å / Rmerge(I) obs: 2.473 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2028

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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: 2.242→48.266 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 1998 4.83 %
Rwork0.2151 39386 -
obs0.2174 41384 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.27 Å2 / Biso mean: 70 Å2 / Biso min: 29.59 Å2
Refinement stepCycle: final / Resolution: 2.242→48.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 198 1 128 5517
Biso mean--49.47 59.21 -
Num. residues----655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125516
X-RAY DIFFRACTIONf_angle_d1.5327530
X-RAY DIFFRACTIONf_chiral_restr0.094879
X-RAY DIFFRACTIONf_plane_restr0.011932
X-RAY DIFFRACTIONf_dihedral_angle_d16.7553316
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.242-2.2980.4311360.4011264995
2.298-2.36020.41081360.3407271898
2.3602-2.42960.38581400.3199274399
2.4296-2.5080.35361390.2925273899
2.508-2.59770.32091390.2872273999
2.5977-2.70170.33061400.2675277899
2.7017-2.82460.29431430.27572804100
2.8246-2.97350.34761400.26132784100
2.9735-3.15980.28261420.25292787100
3.1598-3.40370.31171460.23652865100
3.4037-3.74610.2571430.21172831100
3.7461-4.28790.21951470.1852884100
4.2879-5.40110.22911480.15992938100
5.4011-48.2660.19431590.17533128100
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)
10.0474-0.08140.01240.1707-0.00010.1151-0.034-0.02870.17710.01650.1463-0.1038-0.0364-0.08050.10611.31980.03480.47830.18850.03860.582817.535637.1434-24.7329
20.2153-0.1140.12310.268-0.08350.069-0.13830.17990.0636-0.2474-0.0403-0.26850.04630.1264-0.30291.3749-0.1070.5714-0.05090.18840.561318.66126.5032-37.278
30.081-0.0648-0.05040.1360.06660.02470.04710.02170.1223-0.31-0.0515-0.3615-0.00790.0202-0.16071.24340.05980.4878-0.0161-0.00380.615813.274616.651-38.9762
40.18310.0653-0.08990.7785-0.37210.6567-0.10710.0963-0.1718-0.18610.05020.49770.2255-0.13510.04960.363-0.02310.03080.3468-0.0070.6081-18.879912.1547-13.4104
50.3357-0.2857-0.09590.478-0.01750.2518-0.0054-0.07090.0582-0.10230.01320.157-0.1133-0.13960.00020.49520.0475-0.03090.3327-0.00790.4044-11.769231.2212-14.5133
60.4610.0346-0.13180.3869-0.08440.11960.1503-0.14880.2113-0.4524-0.0761-0.4202-0.0913-0.12490.18011.01720.22560.18020.15950.17920.2655-3.15637.009-34.1953
70.22590.0637-0.11250.26820.10190.1287-0.15020.24790.0626-0.1075-0.39680.025-0.13620.2085-0.08150.83390.0414-0.11050.54890.20790.5838-8.252130.2676-23.0268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 80 through 126 )A80 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 185 )A127 - 185
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 234 )A186 - 234
4X-RAY DIFFRACTION4chain 'A' and (resid 235 through 427 )A235 - 427
5X-RAY DIFFRACTION5chain 'A' and (resid 428 through 598 )A428 - 598
6X-RAY DIFFRACTION6chain 'A' and (resid 599 through 725 )A599 - 725
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 9 )C1 - 9

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