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- PDB-6k6s: Structure of RNase J1 from Staphylococcus epidermidis -

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Basic information

Entry
Database: PDB / ID: 6k6s
TitleStructure of RNase J1 from Staphylococcus epidermidis
ComponentsRibonuclease J 1
KeywordsMETAL BINDING PROTEIN / Ribonuclease / RNase J1
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, conserved site / Uncharacterized protein family UPF0036 signature. / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal 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, conserved site / Uncharacterized protein family UPF0036 signature. / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal 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 1
Similarity search - Component
Biological speciesStaphylococcus epidermidis ATCC 12228 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.993 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 4, 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 1
B: Ribonuclease J 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7196
Polymers127,4992
Non-polymers2204
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-31 kcal/mol
Surface area36580 Å2
Unit cell
Length a, b, c (Å)86.068, 86.068, 486.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsDimer in solution

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Components

#1: Protein Ribonuclease J 1 / RNase J1


Mass: 63749.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis ATCC 12228 (bacteria)
Strain: ATCC 12228 / Gene: rnj1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8CT16, 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

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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: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 10mM Citric acid, 70mM Bis-Tris propane pH 9.3, 20% PEG 3350, 0.1M spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.99→50.581 Å / Num. obs: 21554 / % possible obs: 95.4 % / Redundancy: 6.2 % / CC1/2: 0.971 / Net I/σ(I): 19.8
Reflection shellResolution: 2.99→3.17 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3405 / CC1/2: 0.764 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.993→50.581 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.12
RfactorNum. reflection% reflection
Rfree0.3374 958 4.99 %
Rwork0.2966 --
obs0.2987 19203 83.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.993→50.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5833 0 4 0 5837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035978
X-RAY DIFFRACTIONf_angle_d0.8688225
X-RAY DIFFRACTIONf_dihedral_angle_d13.4061842
X-RAY DIFFRACTIONf_chiral_restr0.031974
X-RAY DIFFRACTIONf_plane_restr0.0041120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.993-3.15080.41241370.37522891X-RAY DIFFRACTION96
3.1508-3.34820.39931510.37422897X-RAY DIFFRACTION96
3.3482-3.60660.46331100.38352172X-RAY DIFFRACTION71
3.6066-3.96940.3914540.37991264X-RAY DIFFRACTION41
3.9694-4.54350.37411620.29042941X-RAY DIFFRACTION95
4.5435-5.72310.30741580.27352959X-RAY DIFFRACTION94
5.7231-50.85780.29571860.26413121X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16020.832-0.27373.6762-0.33341.2330.232-0.2263-0.349-0.6548-0.3029-0.1261-0.42420.2179-0.14280.8095-0.4056-0.110.52750.61640.8849-9.5879-17.9097-26.9132
20.90890.53830.11861.53840.18252.73210.0752-0.1416-0.12150.0771-0.13270.1077-0.1685-0.05490.05660.48290.287-0.00170.82590.32510.6686-12.9022-33.5121-17.6399
31.9873-0.10261.06952.08711.21051.85740.26410.90110.1744-0.0322-0.113-0.53210.3019-0.3762-0.13340.8262-0.3045-0.08531.10150.27640.7696-59.2477-43.2177-32.6568
41.22710.20160.55660.15370.12470.23080.18360.4707-0.2156-0.02940.35720.82260.1138-1.18310.10420.3132-0.38720.14851.50140.38830.9511-66.6679-40.9005-22.2738
51.16550.372-0.02630.729-0.12391.17060.22840.28021.3320.2637-0.60920.3409-0.3096-0.571-0.51040.2998-0.7360.35391.00370.77940.5774-53.625-42.5618-11.9782
62.00141.07370.03761.6095-0.29181.3244-0.2077-0.1990.20290.03670.3710.5126-0.5462-0.5457-0.14330.59040.08210.10170.69870.0790.6066-55.5409-18.5934-16.3035
74.1793-1.73230.20615.4093-0.09781.98010.30880.6466-0.8875-0.7224-0.3137-1.2945-0.290.20490.13850.78240.1468-0.12680.73690.14920.8911-41.5586-16.2315-22.0959
81.10260.4214-0.35641.0721-0.13261.2277-0.269-0.0843-0.048-0.25690.1107-0.43320.67450.43240.07950.6658-0.028-0.00130.86990.28850.6111-48.3561-52.0635-21.6727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 446 )
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 110 )
4X-RAY DIFFRACTION4chain 'B' and (resid 111 through 147 )
5X-RAY DIFFRACTION5chain 'B' and (resid 148 through 221 )
6X-RAY DIFFRACTION6chain 'B' and (resid 222 through 281 )
7X-RAY DIFFRACTION7chain 'B' and (resid 282 through 361 )
8X-RAY DIFFRACTION8chain 'B' and (resid 362 through 445 )

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