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- PDB-7wnt: RNase J from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7wnt
TitleRNase J from Mycobacterium tuberculosis
ComponentsRibonuclease J
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA endonuclease activity / beta-lactamase / beta-lactamase activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal 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
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsLi, J. / Bao, L. / Hu, J. / Zhan, B. / Li, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500600 China
CitationJournal: To Be Published
Title: Structural ans functional study of RNase J from Mycobacterium tuberculosis
Authors: Li, J. / Hu, J. / Bao, L. / Zhan, B.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7323
Polymers59,6011
Non-polymers1312
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-79 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.520, 128.520, 184.276
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-741-

HOH

21A-785-

HOH

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Components

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


Mass: 59601.332 Da / Num. of mol.: 1
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, Hydrolases; Acting on ester bonds, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
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: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES (pH 7.5) 4.3 M NaCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.44→47.64 Å / Num. obs: 33845 / % possible obs: 99.65 % / Redundancy: 2 % / Biso Wilson estimate: 58.61 Å2 / Rmerge(I) obs: 0.01581 / Net I/σ(I): 22.93
Reflection shellResolution: 2.44→2.52 Å / Rmerge(I) obs: 0.2589 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 3269

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Processing

Software
NameVersionClassification
XDS1.13_2998data reduction
XDS1.13_2998data scaling
PHENIX1.10-2155-000phasing
PHENIX1.10-2155-000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZQ4
Resolution: 2.44→47.64 Å / SU ML: 0.3608 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3153 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2509 1628 4.82 %
Rwork0.2193 32165 -
obs0.2208 33793 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.79 Å2
Refinement stepCycle: LAST / Resolution: 2.44→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 2 86 3970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093951
X-RAY DIFFRACTIONf_angle_d1.02555379
X-RAY DIFFRACTIONf_chiral_restr0.0666643
X-RAY DIFFRACTIONf_plane_restr0.0066706
X-RAY DIFFRACTIONf_dihedral_angle_d19.74771422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.520.37861170.33252585X-RAY DIFFRACTION98.08
2.52-2.60.32321270.30522636X-RAY DIFFRACTION99.93
2.6-2.690.35721350.30082628X-RAY DIFFRACTION99.93
2.69-2.80.36561440.28852641X-RAY DIFFRACTION99.86
2.8-2.930.32861360.28682641X-RAY DIFFRACTION99.89
2.93-3.080.34481410.28382630X-RAY DIFFRACTION99.75
3.08-3.270.31091460.25832646X-RAY DIFFRACTION99.79
3.27-3.530.28541350.2232668X-RAY DIFFRACTION99.61
3.53-3.880.23311360.20212682X-RAY DIFFRACTION99.75
3.88-4.440.19041250.1832734X-RAY DIFFRACTION99.79
4.44-5.590.20561430.17922746X-RAY DIFFRACTION99.86
5.59-47.640.21161430.20132928X-RAY DIFFRACTION99.77

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