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- PDB-3zq4: Unusual, dual endo- and exo-nuclease activity in the degradosome ... -

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Basic information

Entry
Database: PDB / ID: 3zq4
TitleUnusual, dual endo- and exo-nuclease activity in the degradosome explained by crystal structure analysis of RNase J1
ComponentsRIBONUCLEASE J 1
KeywordsHYDROLASE / RNA MATURATION
Function / homology
Function and homology information


5'-3' RNA exonuclease activity / RNA endonuclease activity / mRNA processing / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Ribonuclease J, conserved site / Uncharacterized protein family UPF0036 signature. / Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / 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 ...Ribonuclease J, conserved site / Uncharacterized protein family UPF0036 signature. / Ubiquitin-like (UB roll) - #580 / Metallo-hydrolase/oxidoreductase / 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 / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Ubiquitin-like (UB roll) / 4-Layer Sandwich / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNewman, J.A. / Hewitt, L. / Rodrigues, C. / Solovyova, A. / Harwood, C.R. / Lewis, R.J.
CitationJournal: Structure / Year: 2011
Title: Unusual, Dual Endo- and Exonuclease Activity in the Degradosome Explained by Crystal Structure Analysis of Rnase J1.
Authors: Newman, J.A. / Hewitt, L. / Rodrigues, C. / Solovyova, A. / Harwood, C.R. / Lewis, R.J.
History
DepositionJun 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_conn_angle ...entity_src_gen / pdbx_struct_conn_angle / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_type.id
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_data_processing_status.task_name
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE J 1
C: RIBONUCLEASE J 1
D: RIBONUCLEASE J 1
E: RIBONUCLEASE J 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,05416
Polymers246,3704
Non-polymers68412
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15490 Å2
ΔGint-383.2 kcal/mol
Surface area84280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.823, 209.430, 74.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-517-

GLU

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 7:439 )
211CHAIN C AND (RESSEQ 7:439 )
311CHAIN D AND (RESSEQ 7:439 )
411CHAIN E AND (RESSEQ 7:439 )
112CHAIN A AND (RESSEQ 465:474 OR RESSEQ 479:492 OR RESSEQ...
212CHAIN C AND (RESSEQ 465:474 OR RESSEQ 479:492 OR RESSEQ...
312CHAIN D AND (RESSEQ 465:474 OR RESSEQ 479:492 OR RESSEQ...
412CHAIN E AND (RESSEQ 465:474 OR RESSEQ 479:492 OR RESSEQ...

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.6833, 0.7129, 0.1577), (0.7034, 0.585, 0.4038), (0.1956, 0.3869, -0.9012)43.9974, -41.3802, 85.6027
2given(-0.9817, 0.03114, -0.1881), (0.04905, -0.9121, -0.407), (-0.1842, -0.4088, 0.8938)103.477, 92.6867, 30.271
3given(0.6659, -0.7455, -0.02656), (-0.746, -0.6657, -0.01941), (-0.003214, 0.03274, -0.9995)44.5042, 98.1649, 114.186

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Components

#1: Protein
RIBONUCLEASE J 1 / RNASE J1


Mass: 61592.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q45493, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 3.16 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 8
Details: 0.2 M CACL2, 0.1 M TRIS.HCL, PH 8.0, 10 % (W/V) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9804
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 55920 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 61.71 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.5_2)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BK1

3bk1


Resolution: 3→29.76 Å / SU ML: 0.39 / σ(F): 0.52 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 2830 5.1 %
Rwork0.214 --
obs0.216 55828 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.11 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-19.6085 Å20 Å20 Å2
2---12.9032 Å20 Å2
3----6.7053 Å2
Refinement stepCycle: LAST / Resolution: 3→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16889 0 12 0 16901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117196
X-RAY DIFFRACTIONf_angle_d1.32423234
X-RAY DIFFRACTIONf_dihedral_angle_d19.9826421
X-RAY DIFFRACTIONf_chiral_restr0.0992646
X-RAY DIFFRACTIONf_plane_restr0.0063033
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3347X-RAY DIFFRACTIONPOSITIONAL
12C3347X-RAY DIFFRACTIONPOSITIONAL0.054
13D3347X-RAY DIFFRACTIONPOSITIONAL0.051
14E3347X-RAY DIFFRACTIONPOSITIONAL0.049
21A551X-RAY DIFFRACTIONPOSITIONAL
22C551X-RAY DIFFRACTIONPOSITIONAL0.095
23D567X-RAY DIFFRACTIONPOSITIONAL0.092
24E567X-RAY DIFFRACTIONPOSITIONAL0.09
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.10710.36812960.31275201X-RAY DIFFRACTION99
3.1071-3.23140.35992750.29815279X-RAY DIFFRACTION100
3.2314-3.37830.31262880.26755256X-RAY DIFFRACTION100
3.3783-3.55610.32582660.25015286X-RAY DIFFRACTION100
3.5561-3.77850.29522880.22125262X-RAY DIFFRACTION100
3.7785-4.06960.25632770.2065274X-RAY DIFFRACTION100
4.0696-4.47790.20662800.17665328X-RAY DIFFRACTION100
4.4779-5.1230.20762950.1615294X-RAY DIFFRACTION99
5.123-6.44360.21862720.17935354X-RAY DIFFRACTION99
6.4436-29.7580.21692930.19875464X-RAY DIFFRACTION97

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