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- PDB-8yyf: RNase J2 mutant H76A -

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Basic information

Entry
Database: PDB / ID: 8yyf
TitleRNase J2 mutant H76A
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
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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


Theoretical massNumber of molelcules
Total (without water)64,3121
Polymers64,3121
Non-polymers00
Water7,116395
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.040, 72.430, 106.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribonuclease J 2 / RNase J2


Mass: 64312.258 Da / Num. of mol.: 1 / Mutation: H76A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
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: 1.71 Å3/Da / Density % sol: 27.96 %
Crystal growTemperature: 293 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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→42.89 Å / Num. obs: 80710 / % possible obs: 90.4 % / Redundancy: 7.7 % / CC1/2: 0.98 / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.6
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 7.3 % / Num. unique obs: 11475 / CC1/2: 0.95 / % possible all: 89.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→42.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.057 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20464 4005 5 %RANDOM
Rwork0.16473 ---
obs0.16676 76631 90.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2---0.07 Å20 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.39→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 0 395 3757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123431
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.6274642
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.5761011
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62810589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022544
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.0942.1221768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it11.6283.1142207
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.8862.1151663
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.45638.94915015
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr21.97133431
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 309 -
Rwork0.171 6190 -
obs--99.98 %

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