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- PDB-7dcy: Apo form of Mycoplasma genitalium RNase R -

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Basic information

Entry
Database: PDB / ID: 7dcy
TitleApo form of Mycoplasma genitalium RNase R
ComponentsRibonuclease R
KeywordsHYDROLASE / RNA hydrolase / RNA 2'-O-methylation sensitive
Function / homology
Function and homology information


exoribonuclease II / exoribonuclease II activity / miRNA catabolic process / mRNA catabolic process / P-body / 3'-5'-RNA exonuclease activity / 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
Biological speciesMycoplasma genitalium G37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 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
DepositionOct 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6642
Polymers85,6401
Non-polymers241
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.652, 80.768, 176.476
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: 85639.562 Da / Num. of mol.: 1
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: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.9 Å3/Da / Density % sol: 57.56 %
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: Oct 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 70690 / % possible obs: 99.9 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 18.6
Reflection shellResolution: 1.97→2.01 Å / Rmerge(I) obs: 2.931 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3444

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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: 1.972→47.55 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 3689 5.23 %
Rwork0.1733 66893 -
obs0.1747 70582 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.14 Å2 / Biso mean: 43.9301 Å2 / Biso min: 18.04 Å2
Refinement stepCycle: final / Resolution: 1.972→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5199 0 1 475 5675
Biso mean--49.33 49.59 -
Num. residues----644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115341
X-RAY DIFFRACTIONf_angle_d0.9787250
X-RAY DIFFRACTIONf_chiral_restr0.065836
X-RAY DIFFRACTIONf_plane_restr0.006935
X-RAY DIFFRACTIONf_dihedral_angle_d14.3363250
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.972-1.9980.30461110.2931223287
1.998-2.02530.30461180.26872569100
2.0253-2.05430.27941440.25952531100
2.0543-2.08490.27741290.24752567100
2.0849-2.11750.31311550.22782556100
2.1175-2.15220.24121410.21032533100
2.1522-2.18940.22671480.21322574100
2.1894-2.22920.25181480.19952534100
2.2292-2.2720.2251190.19212588100
2.272-2.31840.26881490.19332584100
2.3184-2.36880.23481270.18222573100
2.3688-2.42390.21471480.18892532100
2.4239-2.48450.23921380.18372583100
2.4845-2.55170.21931450.182540100
2.5517-2.62680.21711700.17582545100
2.6268-2.71160.24311500.1792576100
2.7116-2.80850.21511460.18112576100
2.8085-2.92090.20511510.18012569100
2.9209-3.05380.19991410.182585100
3.0538-3.21480.22011410.17612604100
3.2148-3.41620.19891390.1732601100
3.4162-3.67980.17281420.16212635100
3.6798-4.050.16511370.15012617100
4.05-4.63560.1651530.13462629100
4.6356-5.83870.17081310.1532680100
5.8387-100.16831680.1649278099
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)
10.10250.0659-0.00250.0988-0.00230.12460.06040.0732-0.39090.1878-0.0517-0.1202-0.08350.19580.00090.27170.03250.00470.28580.02740.399129.336543.312595.8783
20.30310.1069-0.07920.36970.0620.2405-0.01170.2226-0.0409-0.08090.0177-0.0764-0.00610.00260.00020.2256-0.00930.01020.315-0.01040.267615.47154.312689.745
30.6267-0.0038-0.25250.5543-0.40410.7994-0.0113-0.0452-0.06490.17660.06390.0781-0.0849-0.13230.00010.2751-0.01760.02090.21060.02210.23886.55547.7769129.226
40.64840.6529-0.46550.7874-0.35740.9276-0.0489-0.0916-0.17320.01160.0175-0.1325-0.01140.1841-00.22540.0039-0.00820.255-0.00370.265726.992852.693119.7523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 126 )A82 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 204 )A127 - 204
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 427 )A205 - 427
4X-RAY DIFFRACTION4chain 'A' and (resid 428 through 725 )A428 - 725

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