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- PDB-5ws2: Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNas... -

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Basic information

Entry
Database: PDB / ID: 5ws2
TitleCrystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, complex with RNA
Components
  • RNA (5'-R(P*AP*AP*AP*AP*A)-3')
  • Ribonuclease J
KeywordsHYDROLASE / EXORIBONUCLEASE / BETA-CASP / MBL
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA catabolic process / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribonuclease J, archaea / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
RNA / Ribonuclease J
Similarity search - Component
Biological speciesMethanolobus psychrophilus R15 (archaea)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsLi, D.F. / Feng, N.
CitationJournal: Mol. Microbiol. / Year: 2017
Title: New molecular insights into an archaeal RNase J reveal a conserved processive exoribonucleolysis mechanism of the RNase J family
Authors: Zheng, X. / Feng, N. / Li, D. / Dong, X. / Li, J.
History
DepositionDec 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease J
B: Ribonuclease J
C: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
D: RNA (5'-R(P*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,65717
Polymers107,5314
Non-polymers1,12613
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-297 kcal/mol
Surface area35980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.610, 168.610, 165.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Ribonuclease J / RNase J


Mass: 52164.453 Da / Num. of mol.: 2 / Mutation: S247A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanolobus psychrophilus R15 (archaea)
Gene: rnj, Mpsy_0886 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: K4MAF9, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*A)-3')


Mass: 1601.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.01M MgSO4, 0.05M Sodium cacodylate trihydrate, 2M (NH4)2SO4
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2016
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 54889 / % possible obs: 100 % / Redundancy: 16.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.172 / Net I/σ(I): 17.3
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 5 / CC1/2: 0.903 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HAB

5hab


Resolution: 2.398→48.674 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 2000 3.68 %Random
Rwork0.1731 ---
obs0.1745 54405 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.398→48.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7207 222 49 312 7790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097628
X-RAY DIFFRACTIONf_angle_d1.18210384
X-RAY DIFFRACTIONf_dihedral_angle_d23.4212848
X-RAY DIFFRACTIONf_chiral_restr0.0751185
X-RAY DIFFRACTIONf_plane_restr0.0091306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3976-2.45760.26631390.21393667X-RAY DIFFRACTION99
2.4576-2.5240.29391420.20693702X-RAY DIFFRACTION100
2.524-2.59830.28031420.1943716X-RAY DIFFRACTION100
2.5983-2.68220.25561410.20013692X-RAY DIFFRACTION100
2.6822-2.7780.21151420.20063723X-RAY DIFFRACTION100
2.778-2.88920.26581420.20413714X-RAY DIFFRACTION100
2.8892-3.02070.23031420.19223738X-RAY DIFFRACTION100
3.0207-3.180.23361440.18833748X-RAY DIFFRACTION100
3.18-3.37910.20021430.17623760X-RAY DIFFRACTION100
3.3791-3.640.22641440.17093758X-RAY DIFFRACTION100
3.64-4.00610.21261440.16133787X-RAY DIFFRACTION100
4.0061-4.58540.16331450.13953783X-RAY DIFFRACTION100
4.5854-5.77570.17571440.15393801X-RAY DIFFRACTION98
5.7757-48.68350.17351460.17053816X-RAY DIFFRACTION94
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)
12.1298-0.73142.10521.3564-0.62823.28680.20550.3372-0.1734-0.0936-0.25590.04070.21970.3230.04680.29610.08270.0920.35630.0150.315964.805344.92491.685
21.1089-0.266-0.08410.8550.01151.2395-0.01020.1798-0.1594-0.1449-0.03650.01360.27530.01340.04090.30230.0340.0320.2579-0.06160.264243.1332345.083-3.2132
34.5533-1.36633.35130.3946-1.02612.4263-0.3247-0.2478-0.28880.03810.54960.0817-0.3829-0.3409-0.19750.3515-0.0270.00270.5541-0.00780.397-7.0913380.09596.0492
42.5221.2546-1.29163.63190.40331.66120.1059-0.2641-0.03790.3109-0.1022-0.0363-0.0478-0.14870.00090.2520.05550.05840.55550.03640.275813.3254365.51534.4229
51.8705-0.6952-0.52162.54680.10480.28160.0077-0.00710.02920.24470.01450.2170.0727-0.4606-0.01330.2433-0.03960.07890.56790.01160.39235.913356.561824.9107
61.8617-1.37320.9052.5985-1.30221.9746-0.03820.0061-0.3069-0.02650.07610.17370.3206-0.3904-0.03670.2472-0.07640.0850.3417-0.02660.318621.8115345.206121.2942
74.10520.62130.16861.97440.35382.42110.0312-0.5784-0.35310.4648-0.02420.12310.4633-0.1381-0.030.40270.02410.07910.31410.08670.300533.5006340.941335.0276
80.26230.0109-0.28850.01560.02130.3636-0.06460.03790.1940.05010.0114-0.0320.04610.00420.04110.24270.04410.02370.2928-0.0020.316337.665352.454425.6156
92.11440.3859-0.37242.71490.34520.8372-0.07780.17930.1477-0.10980.00650.2877-0.1484-0.48340.09070.20190.0836-0.00030.51080.06470.278412.5125370.012611.8931
106.2-1.52945.05245.0324-2.08235.3973-0.22250.48670.56040.397-0.2774-0.45290.19981.08110.45120.59930.1245-0.06780.595-0.0730.741642.1543353.0719-8.7553
117.0826-3.88066.99936.016-2.72847.2724-0.24510.20330.48520.80990.36960.2731-1.4338-0.6361-0.160.52780.01410.10770.49970.03360.715826.1595355.710332.7203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -19 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 448 )
3X-RAY DIFFRACTION3chain 'B' and (resid -14 through 10 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 118 )
5X-RAY DIFFRACTION5chain 'B' and (resid 119 through 182 )
6X-RAY DIFFRACTION6chain 'B' and (resid 183 through 282 )
7X-RAY DIFFRACTION7chain 'B' and (resid 283 through 358 )
8X-RAY DIFFRACTION8chain 'B' and (resid 359 through 390 )
9X-RAY DIFFRACTION9chain 'B' and (resid 391 through 448 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 5 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 5 )

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