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- PDB-6k6w: Structure of RNase J2 from Staphylococcus epidermidis -

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Basic information

Entry
Database: PDB / ID: 6k6w
TitleStructure of RNase J2 from Staphylococcus epidermidis
ComponentsRibonuclease J 2
KeywordsMETAL 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
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 / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Metallo-beta-lactamase superfamily ...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 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Ribonuclease J 2
Similarity search - Component
Biological speciesStaphylococcus epidermidis ATCC 12228 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRaj, R. / Gopal, B.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure of RNase J1 from Staphylococcus epidermidis
Authors: Raj, R. / Gopal, B.
History
DepositionJun 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water2,036113
1
A: Ribonuclease J 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4342
Polymers64,3791
Non-polymers551
Water181
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
Water181
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
Water181
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
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.550, 131.040, 115.900
Angle α, β, γ (deg.)90.00, 91.72, 90.00
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 epidermidis ATCC 12228 (bacteria)
Strain: ATCC 12228 / Gene: rnj2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8CST0, 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.35 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 100mM tri-sodium citrate dihydrate pH 5.6, 20% PEG 4000, 20% Isopropanol, 40% Formamide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→36.39 Å / Num. obs: 47771 / % possible obs: 90.6 % / Redundancy: 5.6 % / CC1/2: 0.986 / Rsym value: 0.143 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.7 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 3949 / CC1/2: 0.744 / Rsym value: 0.719 / % possible all: 81.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→36.39 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8
RfactorNum. reflection% reflection
Rfree0.2546 2295 4.82 %
Rwork0.2002 --
obs0.2028 47629 90.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→36.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13286 0 4 113 13403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413563
X-RAY DIFFRACTIONf_angle_d0.86318398
X-RAY DIFFRACTIONf_dihedral_angle_d13.4684846
X-RAY DIFFRACTIONf_chiral_restr0.0312135
X-RAY DIFFRACTIONf_plane_restr0.0032384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.75870.32971320.2532519X-RAY DIFFRACTION81
2.7587-2.82290.30951270.24082541X-RAY DIFFRACTION81
2.8229-2.89340.3241280.24452578X-RAY DIFFRACTION82
2.8934-2.97160.30011340.23272609X-RAY DIFFRACTION83
2.9716-3.0590.28241620.23082610X-RAY DIFFRACTION84
3.059-3.15770.26651480.23532666X-RAY DIFFRACTION87
3.1577-3.27050.2961370.22162737X-RAY DIFFRACTION87
3.2705-3.40130.27561450.21482823X-RAY DIFFRACTION89
3.4013-3.5560.26741250.20942879X-RAY DIFFRACTION92
3.556-3.74330.22071420.19532987X-RAY DIFFRACTION94
3.7433-3.97760.22651290.18723032X-RAY DIFFRACTION96
3.9776-4.28430.23711360.17613059X-RAY DIFFRACTION97
4.2843-4.71460.21791630.16743041X-RAY DIFFRACTION97
4.7146-5.39490.22331750.18073048X-RAY DIFFRACTION97
5.3949-6.78980.28351800.22363053X-RAY DIFFRACTION97
6.7898-36.39350.23811320.18163152X-RAY DIFFRACTION97

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