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- PDB-7wnu: Mycobacterium tuberculosis Rnase J complex with 7nt RNA -

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Basic information

Entry
Database: PDB / ID: 7wnu
TitleMycobacterium tuberculosis Rnase J complex with 7nt RNA
Components
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')
  • Ribonuclease J
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA endonuclease activity / beta-lactamase activity / beta-lactamase / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / : / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J, beta-CASP domain / Ribonuclease J / Ribonuclease J, domain 2 / Beta-lactamase superfamily domain ...Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / : / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J, beta-CASP domain / Ribonuclease J / Ribonuclease J, domain 2 / Beta-lactamase superfamily domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Ubiquitin-like (UB roll) / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Ribonuclease J
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLi, J. / Hu, J. / Bao, L. / Zhan, B. / Li, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500600 China
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into RNase J that plays an essential role in Mycobacterium tuberculosis RNA metabolism
Authors: Bao, L. / Hu, J. / Zhan, B. / Chi, M. / Li, Z. / Wang, S. / Shan, C. / Zhao, Z. / Guo, Y. / Ding, X. / Ji, C. / Tao, S. / Ni, T. / Zhang, X. / Zhao, G. / Li, J.
History
DepositionJan 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,9838
Polymers123,7224
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-163 kcal/mol
Surface area42720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.060, 145.380, 192.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Ribonuclease J / RNase J / Beta-lactamase / Penicillinase


Mass: 59601.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: rnj / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGZ9, beta-lactamase
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 2259.483 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.2→42.88 Å / Num. obs: 21660 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 59.25 Å2 / Rmerge(I) obs: 0.0405 / Net I/σ(I): 16.77
Reflection shellResolution: 3.2→3.314 Å / Rmerge(I) obs: 0.156 / Num. unique obs: 2157

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZQ4

3zq4


Resolution: 3.2→42.88 Å / SU ML: 0.3647 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2406 1067 4.93 %
Rwork0.1851 20564 -
obs0.1879 21631 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.03 Å2
Refinement stepCycle: LAST / Resolution: 3.2→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8250 286 4 0 8540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01078721
X-RAY DIFFRACTIONf_angle_d1.343211928
X-RAY DIFFRACTIONf_chiral_restr0.07781427
X-RAY DIFFRACTIONf_plane_restr0.01221514
X-RAY DIFFRACTIONf_dihedral_angle_d23.00093230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.350.33221140.2492547X-RAY DIFFRACTION99.74
3.35-3.520.27381540.22342500X-RAY DIFFRACTION99.92
3.52-3.740.27771310.2022577X-RAY DIFFRACTION100
3.74-4.030.23171330.18062519X-RAY DIFFRACTION99.96
4.03-4.440.23031370.16472547X-RAY DIFFRACTION99.93
4.44-5.080.19551110.15182607X-RAY DIFFRACTION99.96
5.08-6.390.21741340.19052590X-RAY DIFFRACTION100
6.39-42.880.23971530.17742677X-RAY DIFFRACTION99.37

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