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- PDB-7did: Mycoplasma genitalium RNase R in complex with ribose methylated s... -

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Basic information

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


exoribonuclease II / exoribonuclease II activity / RNA metabolic 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 / S1 domain profile. ...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: 1.9 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(*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9063
Polymers86,8812
Non-polymers241
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-13 kcal/mol
Surface area30780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.286, 80.784, 175.735
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(*AP*AP*AP*A)-3')


Mass: 1285.893 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 / Water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
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: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 78483 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 18
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3891 / Rrim(I) all: 2.936

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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: 1.9→29.979 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1995 2.55 %
Rwork0.1881 76281 -
obs0.189 78276 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.49 Å2 / Biso mean: 46.0262 Å2 / Biso min: 21.1 Å2
Refinement stepCycle: final / Resolution: 1.9→29.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 86 1 493 5776
Biso mean--39.6 49.03 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125405
X-RAY DIFFRACTIONf_angle_d1.0097347
X-RAY DIFFRACTIONf_chiral_restr0.067851
X-RAY DIFFRACTIONf_plane_restr0.006929
X-RAY DIFFRACTIONf_dihedral_angle_d15.5483261
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.94720.40591390.3518528398
1.9472-1.99980.34211420.30545422100
1.9998-2.05870.31851410.28085389100
2.0587-2.12510.31671420.2555434100
2.1251-2.2010.26191410.22915373100
2.201-2.28910.26871410.21195409100
2.2891-2.39330.25581420.20015434100
2.3933-2.51940.23091430.19325421100
2.5194-2.67710.21991410.1885440100
2.6771-2.88370.24391430.19455464100
2.8837-3.17360.22771430.19415452100
3.1736-3.63210.21221420.1765501100
3.6321-4.57350.1721460.15325549100
4.5735-29.970.19411490.1665571099
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)
11.85470.90370.55491.216-0.52080.9071-0.0175-0.01810.41130.1117-0.00310.2356-0.1909-0.14710.00020.26360.0099-0.01710.2715-0.01950.3204-24.6253-7.57054.3733
21.08690.1932-0.97040.75460.53221.38680.06520.10540.062-0.0084-0.0224-0.0932-0.06290.12170.00610.2195-0.0273-0.00310.2810.00080.2666-7.5075-14.22128.3352
31.8730.32450.42162.050.32882.0706-0.0727-0.2231-0.01420.36930.0124-0.11850.16710.0886-0.00110.37810.0149-0.04690.2628-0.03560.2826-6.7136-5.573947.7015
41.04040.82020.5091.14050.51171.2809-0.0876-0.10960.28960.04440.01120.2381-0.0623-0.2615-0.00030.23750.0132-0.01510.28140.0090.2761-26.913-11.859831.4631
50.0074-0.01940.00240.0269-0.00920.01460.0705-0.0451-0.51630.29650.2138-0.56771.00120.6208-0.00030.8362-0.0739-0.24650.76020.14921.4781-19.407-9.663638.8457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 170 )A82 - 170
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 250 )A171 - 250
3X-RAY DIFFRACTION3chain 'A' and (resid 251 through 427 )A251 - 427
4X-RAY DIFFRACTION4chain 'A' and (resid 428 through 725 )A428 - 725
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 8 )C5 - 8

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