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- PDB-5a0v: Catalysis and 5' end sensing by ribonuclease RNase J of the metal... -

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Basic information

Entry
Database: PDB / ID: 5a0v
TitleCatalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family
Components
  • 5'-R(*CP*GP*CP*CP*UP*CP)-3'
  • RIBONUCLEASE J
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / ENDONUCLEASE / EXONUCLEASE
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 / 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-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 / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / RNA / Ribonuclease J
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPei, X.Y. / Bralley, P. / Jones, G.H. / Luisi, B.F.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Linkage of Catalysis and 5' End Recognition in Ribonuclease Rnase J
Authors: Pei, X.Y. / Bralley, P. / Jones, G.H. / Luisi, B.F.
History
DepositionApr 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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 / _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
B: RIBONUCLEASE J
E: 5'-R(*CP*GP*CP*CP*UP*CP)-3'
F: 5'-R(*CP*GP*CP*CP*UP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5319
Polymers125,9464
Non-polymers5855
Water1,35175
1
A: RIBONUCLEASE J
E: 5'-R(*CP*GP*CP*CP*UP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1044
Polymers62,9732
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-6.7 kcal/mol
Surface area22670 Å2
MethodPQS
2
B: RIBONUCLEASE J
F: 5'-R(*CP*GP*CP*CP*UP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4275
Polymers62,9732
Non-polymers4543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-6 kcal/mol
Surface area22530 Å2
MethodPQS
Unit cell
Length a, b, c (Å)184.130, 184.130, 112.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2866, -0.000552, -0.9581), (0.01946, -0.9998, 0.006397), (-0.9579, -0.02048, -0.2865)
Vector: 0.1156, 120.5, 1.226)

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Components

#1: Protein RIBONUCLEASE J


Mass: 61146.090 Da / Num. of mol.: 2
Fragment: BETA-LACTAMASE DOMAIN AND BETA-CASP DOMAIN, RESIDUES 1-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR A3(2) (bacteria)
Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: O86842
#2: RNA chain 5'-R(*CP*GP*CP*CP*UP*CP)-3'


Mass: 1827.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR A3(2) (bacteria)
Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 4.9 Å3/Da / Density % sol: 0.74 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD
Crystal growpH: 8.5
Details: THE BEST CRYSTALS OF S. COELICOLOR RNASE J WERE OBTAINED IN THE 27.5% W/V PEG 400, 0.1 M TRIS-HCL, PH 8.5 BY MIXING A 1:2 VOLUME RATIO OF CRYSTALLIZATION RESERVOIR TO PROTEIN SOLUTION, THEN SOAKED WITH MNCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91742
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91742 Å / Relative weight: 1
ReflectionResolution: 2.7→2.75 Å / Num. obs: 47608 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 6.9 % / Biso Wilson estimate: 55.49 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A0T

5a0t


Resolution: 2.8→32.719 Å / SU ML: 0.32 / σ(F): 0.05 / Phase error: 20.92 / Stereochemistry target values: ML
Details: DISORDERED REGIONS OF RESIDUES 456 TO 561 IN BOTH A CHAIN AND B CHAIN WERE NOT MODELLED.
RfactorNum. reflection% reflection
Rfree0.2084 4377 4.8 %
Rwork0.1542 --
obs0.1567 39850 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→32.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6950 196 25 75 7246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087332
X-RAY DIFFRACTIONf_angle_d1.17810008
X-RAY DIFFRACTIONf_dihedral_angle_d14.9912753
X-RAY DIFFRACTIONf_chiral_restr0.0471150
X-RAY DIFFRACTIONf_plane_restr0.0061287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.32881560.26712857X-RAY DIFFRACTION100
2.8318-2.86510.3331600.25662873X-RAY DIFFRACTION99
2.8651-2.90.27821580.262838X-RAY DIFFRACTION100
2.9-2.93670.31911380.262872X-RAY DIFFRACTION100
2.9367-2.97530.30981360.24812872X-RAY DIFFRACTION99
2.9753-3.01610.28371350.24632873X-RAY DIFFRACTION99
3.0161-3.05910.29391520.24042896X-RAY DIFFRACTION99
3.0591-3.10470.26771470.22552858X-RAY DIFFRACTION100
3.1047-3.15320.2761650.22622886X-RAY DIFFRACTION100
3.1532-3.20490.23691560.21042860X-RAY DIFFRACTION100
3.2049-3.26010.2511630.19892886X-RAY DIFFRACTION100
3.2601-3.31930.33811290.19132882X-RAY DIFFRACTION100
3.3193-3.38310.24381600.18942884X-RAY DIFFRACTION100
3.3831-3.45210.23641610.1922830X-RAY DIFFRACTION99
3.4521-3.5270.24441370.1632908X-RAY DIFFRACTION99
3.527-3.6090.21481430.162833X-RAY DIFFRACTION99
3.609-3.69910.19171600.14692791X-RAY DIFFRACTION98
3.6991-3.7990.19051400.13842832X-RAY DIFFRACTION98
3.799-3.91060.16021660.12712890X-RAY DIFFRACTION100
3.9106-4.03660.17461450.11882887X-RAY DIFFRACTION100
4.0366-4.18060.16421430.11772916X-RAY DIFFRACTION100
4.1806-4.34760.15211370.10532860X-RAY DIFFRACTION100
4.3476-4.5450.15911410.10222891X-RAY DIFFRACTION100
4.545-4.78390.16591240.10572914X-RAY DIFFRACTION100
4.7839-5.08260.13351220.10362913X-RAY DIFFRACTION100
5.0826-5.47340.16811400.11582854X-RAY DIFFRACTION98
5.4734-6.02110.20641340.13342838X-RAY DIFFRACTION98
6.0211-6.88530.21281590.14432799X-RAY DIFFRACTION97
6.8853-8.64820.17561440.13812789X-RAY DIFFRACTION97
8.6482-32.72110.21831260.16972867X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 16.8119 Å / Origin y: 60.5149 Å / Origin z: -12.4589 Å
111213212223313233
T0.5804 Å20.07 Å20.0373 Å2-0.2785 Å20.0245 Å2--0.4141 Å2
L0.7024 °2-0.1936 °20.7222 °2-0.2408 °2-0.2504 °2--1.5973 °2
S0.0029 Å °0.1417 Å °-0.0883 Å °-0.1209 Å °-0.0159 Å °-0.1389 Å °0.4241 Å °0.3332 Å °0.0125 Å °
Refinement TLS groupSelection details: ALL

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