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- PDB-6llb: Crystal structure of mpy-RNase J (mutant S247A), an archaeal RNas... -

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Basic information

Entry
Database: PDB / ID: 6llb
TitleCrystal structure of mpy-RNase J (mutant S247A), an archaeal RNase J from Methanolobus psychrophilus R15, in complex with 6 nt RNA
Components
  • MPY-RNase J
  • RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / EXORIBONUCLEASE / BETA-CASP / MBL domain / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA
Function and homology information
Biological speciesMethanolobus psychrophilus R15 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, D.F. / Hou, Y.J. / Guo, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31870037 China
CitationJournal: Rna Biol. / Year: 2020
Title: A newly identified duplex RNA unwinding activity of archaeal RNase J depends on processive exoribonucleolysis coupled steric occlusion by its structural archaeal loops.
Authors: Li, J. / Hou, Y. / Gu, X. / Yue, L. / Guo, L. / Li, D. / Dong, X.
History
DepositionDec 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 9, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,31617
Polymers108,1894
Non-polymers1,12613
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-284 kcal/mol
Surface area36700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.726, 168.726, 166.427
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid -14 through 448)
21(chain B and (resid -14 through -6 or resid 0...
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISASPASP(chain A and resid -14 through 448)AA-14 - 4488 - 470
211HISHISPROPRO(chain B and (resid -14 through -6 or resid 0...BB-14 - -68 - 16
221ALAALAARGARG(chain B and (resid -14 through -6 or resid 0...BB0 - 29822 - 320
231ARGARGARGARG(chain B and (resid -14 through -6 or resid 0...BB299321
241HISHISASPASP(chain B and (resid -14 through -6 or resid 0...BB-14 - 4488 - 470
251HISHISASPASP(chain B and (resid -14 through -6 or resid 0...BB-14 - 4488 - 470
261HISHISASPASP(chain B and (resid -14 through -6 or resid 0...BB-14 - 4488 - 470
271HISHISASPASP(chain B and (resid -14 through -6 or resid 0...BB-14 - 4488 - 470
112AAAAchain CCC1 - 61 - 6
212AAAAchain DDD1 - 61 - 6

NCS ensembles :
ID
1
2

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Components

#1: Protein MPY-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)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsAuthors state that the protein used for crystallization is the S247A mutant of Methanolobus ...Authors state that the protein used for crystallization is the S247A mutant of Methanolobus psychrophilus RNase J, with the NCBI reference sequence ID of WP_015052818.1.

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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: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01 M MgSO4, 0.05 M (CH3)2AsO2Na (pH 6.5) and 2 M (NH4)2SO4.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.6→48.71 Å / Num. obs: 43478 / % possible obs: 100 % / Redundancy: 15.4 % / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.021 / Rrim(I) all: 0.085 / Net I/σ(I): 31.7 / Num. measured all: 671046
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.715.70.9387010044590.9330.2420.9694.2100
9.73-48.7112.30.0181191396810.0050.019105.799.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WS2

5ws2


Resolution: 2.6→46.746 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1995 4.6 %Random
Rwork0.188 41409 --
obs0.1897 43404 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.46 Å2 / Biso mean: 61.2789 Å2 / Biso min: 30.71 Å2
Refinement stepCycle: final / Resolution: 2.6→46.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7201 266 49 65 7581
Biso mean--95.29 50.31 -
Num. residues----938
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2784X-RAY DIFFRACTION7.813TORSIONAL
12B2784X-RAY DIFFRACTION7.813TORSIONAL
21C138X-RAY DIFFRACTION7.813TORSIONAL
22D138X-RAY DIFFRACTION7.813TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.6-2.6650.30731390.25722910
2.665-2.73710.3041390.23072885
2.7371-2.81760.26881410.23662916
2.8176-2.90850.32541390.23052899
2.9085-3.01250.24751410.22242935
3.0125-3.13310.28871410.21052902
3.1331-3.27560.23211400.20922927
3.2756-3.44830.26491410.20532932
3.4483-3.66420.22151430.1892952
3.6642-3.9470.21071430.1752953
3.947-4.3440.20121430.16312965
4.344-4.97190.16371440.14932996
4.9719-6.26170.22771480.19023036
6.2617-46.7460.20771530.1823201
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)
12.5874-0.68232.90681.8918-0.61983.34720.35620.2737-0.27860.0384-0.3523-0.09720.590.3680.03270.59010.22940.10720.5970.01870.511471.2169338.40529.115
21.76640.6741-1.61414.50960.77732.157-0.19630.4171-0.0267-0.51820.12090.04150.12890.4080.07530.50960.18740.00950.6634-0.04420.415256.5429348.5334-11.5604
32.6087-0.54470.19411.48050.51311.4682-0.2060.3487-0.3322-0.06320.1270.0841.01850.32430.10950.74730.22720.10270.4889-0.10310.568751.124335.43070.7426
41.3502-0.22340.32642.97590.01312.79690.01830.4016-0.1589-0.2428-0.08540.32160.3403-0.37010.05970.35440.01120.03160.567-0.09190.441727.621351.305-8.3061
52.48210.9604-0.28353.66040.30742.5066-0.2753-0.2724-0.34780.25180.0489-0.20970.70330.68630.18890.50220.24570.01560.5732-0.0060.400158.4847343.972413.099
62.707-0.43341.66090.2669-1.01150.8135-0.3456-0.0271-0.0192-0.10890.60310.075-0.2323-0.2652-0.1160.5023-0.03450.06631.0987-0.02330.6497-7.0582380.44715.9807
72.180.8371-1.27832.63280.28782.5277-0.0003-0.1538-0.08560.3416-0.1194-0.0649-0.1104-0.32670.12950.36270.11860.07440.82310.05070.467213.3321365.769534.5197
83.0586-1.0742-1.3191.34480.18431.7896-0.12730.2353-0.16230.19310.05120.26890.2867-0.75220.12110.3535-0.08370.09720.8057-0.0260.54887.6309356.813420.6083
93.13140.56910.73582.2567-0.57583.3265-0.0107-0.3343-0.35610.3107-0.03080.05460.68-0.22720.02540.5590.02140.1630.34120.03320.50830.8331340.223631.1102
101.2033-0.54330.10961.1343-0.28981.5868-0.0860.19860.0785-0.02540.03080.0725-0.0071-0.40520.08520.2910.05710.08470.52430.00980.397821.2876364.10716.7277
115.7388-1.67520.25134.481-2.96272.044-0.02970.9497-0.31090.1863-0.1619-0.02380.29091.2037-0.25860.99980.14590.06860.8715-0.25841.072241.5647353.0935-11.1787
126.3997-3.05413.09272.7538-0.15512.5916-0.1779-0.0581-0.03160.40670.89950.6846-0.4699-0.8875-0.77850.8946-0.1160.06180.77290.0371.308225.8468354.544734.8418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -19 through 31 )A-19 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 117 )A32 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 218 )A118 - 218
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 390 )A219 - 390
5X-RAY DIFFRACTION5chain 'A' and (resid 391 through 448 )A391 - 448
6X-RAY DIFFRACTION6chain 'B' and (resid -14 through 10 )B-14 - 10
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 118 )B11 - 118
8X-RAY DIFFRACTION8chain 'B' and (resid 119 through 218 )B119 - 218
9X-RAY DIFFRACTION9chain 'B' and (resid 219 through 358 )B219 - 358
10X-RAY DIFFRACTION10chain 'B' and (resid 359 through 448 )B359 - 448
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 6 )C1 - 6
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 6 )D1 - 6

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