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- PDB-8yyk: Structure of RNase J2 wild type at room temperature -

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Basic information

Entry
Database: PDB / ID: 8yyk
TitleStructure of RNase J2 wild type at room temperature
ComponentsRibonuclease J 2
KeywordsRNA BINDING PROTEIN / Ribonuclease / RNase J2
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA endonuclease 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, beta-CASP domain / Ribonuclease J / Ribonuclease J, domain 2 / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily ...: / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J, beta-CASP domain / Ribonuclease J / Ribonuclease J, domain 2 / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / Ribonuclease J 2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSingh, A.K. / Chinnasamy, K. / Gopal, B.
Funding support India, 3items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)FA/DSTO-17-0001.03 India
Department of Science & Technology (DST, India)SP/DSTO-16-1668.03 India
Science and Engineering Research Board (SERB)SP/SERB-23-0307.26 India
CitationJournal: J.Biol.Chem. / Year: 2024
Title: A physicochemical rationale for the varied catalytic efficiency in RNase J paralogues.
Authors: Singh, A.K. / Chinnasamy, K. / Pahelkar, N.R. / Gopal, B.
History
DepositionApr 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease J 2
B: Ribonuclease J 2
C: Ribonuclease J 2
D: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,7378
Polymers257,5174
Non-polymers2204
Water00
1
A: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4342
Polymers64,3791
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4342
Polymers64,3791
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4342
Polymers64,3791
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4342
Polymers64,3791
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.304, 133.380, 117.751
Angle α, β, γ (deg.)90.000, 92.019, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribonuclease J 2 / RNase J2


Mass: 64379.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: rnj2, SERP0842 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5HPR6, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 5.6
Details: 100mM tri-sodium citrate dihydrate pH 5.6, 20% PEG 4000, 20% Isopropanol, 40% Formamide
PH range: 5.6-6.0

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Data collection

DiffractionMean temperature: 278 K
Ambient temp details: Data collected using capillary at non-cryogenic temperature
Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 3.2→58.6 Å / Num. obs: 29972 / % possible obs: 90.1 % / Redundancy: 2.6 % / CC1/2: 0.92 / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.6
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 0.6 / Num. unique obs: 4411 / CC1/2: 0.48

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→58.6 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.842 / SU B: 28.014 / SU ML: 0.451 / Cross valid method: FREE R-VALUE / ESU R Free: 0.564
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2477 1392 4.648 %
Rwork0.2049 28559 -
all0.207 --
obs-29951 89.671 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.488 Å2
Baniso -1Baniso -2Baniso -3
1-0.354 Å20 Å2-0.024 Å2
2--0.568 Å20 Å2
3----0.918 Å2
Refinement stepCycle: LAST / Resolution: 3.2→58.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13034 0 4 0 13038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01213295
X-RAY DIFFRACTIONr_bond_other_d0.0020.01612141
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.62418030
X-RAY DIFFRACTIONr_angle_other_deg0.3681.54728075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41351739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.1071032
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.696102128
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.21210527
X-RAY DIFFRACTIONr_chiral_restr0.040.22108
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022508
X-RAY DIFFRACTIONr_nbd_refined0.2070.22314
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.211387
X-RAY DIFFRACTIONr_nbtor_refined0.1750.26486
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.27168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3320.216
X-RAY DIFFRACTIONr_nbd_other0.330.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.21
X-RAY DIFFRACTIONr_mcbond_it2.4464.2456983
X-RAY DIFFRACTIONr_mcbond_other2.4424.2456983
X-RAY DIFFRACTIONr_mcangle_it4.2226.3598713
X-RAY DIFFRACTIONr_mcangle_other4.2226.3598714
X-RAY DIFFRACTIONr_scbond_it2.4564.2436312
X-RAY DIFFRACTIONr_scbond_other2.4564.2436313
X-RAY DIFFRACTIONr_scangle_it3.9956.3189317
X-RAY DIFFRACTIONr_scangle_other3.9956.3199318
X-RAY DIFFRACTIONr_lrange_it9.40478.03654364
X-RAY DIFFRACTIONr_lrange_other9.40478.03654365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.2820.3591060.2982099X-RAY DIFFRACTION89.6341
3.282-3.3710.339810.2712095X-RAY DIFFRACTION90.9319
3.371-3.4690.376740.2661688X-RAY DIFFRACTION75.1386
3.469-3.5750.243870.241921X-RAY DIFFRACTION89.523
3.575-3.6920.258870.2241603X-RAY DIFFRACTION76.7833
3.692-3.8210.238950.2011811X-RAY DIFFRACTION89.7364
3.821-3.9650.275670.1981493X-RAY DIFFRACTION77.8443
3.965-4.1260.241900.1961779X-RAY DIFFRACTION93.5904
4.126-4.3080.189860.1731682X-RAY DIFFRACTION93.3474
4.308-4.5170.223880.1671605X-RAY DIFFRACTION94.7398
4.517-4.760.201580.1591585X-RAY DIFFRACTION94.4253
4.76-5.0470.223760.1681465X-RAY DIFFRACTION94.3662
5.047-5.3920.229640.1791385X-RAY DIFFRACTION94.644
5.392-5.820.201720.1891283X-RAY DIFFRACTION95.1545
5.82-6.370.279520.211220X-RAY DIFFRACTION95.9276
6.37-7.1110.257670.2231079X-RAY DIFFRACTION96.3025
7.111-8.1910.227510.189976X-RAY DIFFRACTION95.713
8-9.9840.21380.167808X-RAY DIFFRACTION94.5251
9.984-13.9190.165370.179629X-RAY DIFFRACTION93.9351
13.919-58.60.546160.373353X-RAY DIFFRACTION86.4169

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