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- PDB-5a0t: Catalysis and 5' end sensing by ribonuclease RNase J of the metal... -

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Basic information

Entry
Database: PDB / ID: 5a0t
TitleCatalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family
Components
  • 5'-R(*CP*GP*CP*CP*UP)-3'
  • RIBONUCLEASE J
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / RIBONUCLEASE / RNASE J / 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, beta-CASP domain / Ribonuclease J / Ribonuclease J, domain 2 / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain ...Metallo-hydrolase/oxidoreductase / : / Ribonuclease J, bacteria / Ribonuclease J, C-terminal / Ribonuclease J C-terminal domain / Ribonuclease J, beta-CASP 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 Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RNA / Ribonuclease J
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR A3
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.283 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 22, 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)-3'
F: 5'-R(*CP*GP*CP*CP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,42010
Polymers125,9464
Non-polymers4746
Water10,052558
1
A: RIBONUCLEASE J
E: 5'-R(*CP*GP*CP*CP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2105
Polymers62,9732
Non-polymers2373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-104.4 kcal/mol
Surface area18650 Å2
MethodPISA
2
B: RIBONUCLEASE J
F: 5'-R(*CP*GP*CP*CP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2105
Polymers62,9732
Non-polymers2373
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-105.1 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.187, 186.187, 113.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-2024-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, -0.01394, 0.002726), (-0.001394, 0.2872, 0.9579), (-0.01414, 0.9578, -0.2872)
Vector: 121.8, -27.14, 37.41)

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Components

#1: Protein RIBONUCLEASE J


Mass: 61146.090 Da / Num. of mol.: 2
Fragment: BETA-LACTMASE 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)-3'


Mass: 1827.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: ROSETTA2 PLYSS / Strain: BL21(DE3)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: NONE
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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2824
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2.28→35 Å / Num. obs: 88741 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.6
Reflection shellResolution: 2.28→2.3 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
SHELXphasing
PHENIXphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 3BK1

3bk1


Resolution: 2.283→29.34 Å / SU ML: 0.23 / σ(F): 1.21 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 8404 5 %
Rwork0.1446 --
obs0.1463 88509 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.283→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6950 216 18 558 7742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097344
X-RAY DIFFRACTIONf_angle_d1.20610019
X-RAY DIFFRACTIONf_dihedral_angle_d13.8122759
X-RAY DIFFRACTIONf_chiral_restr0.0511150
X-RAY DIFFRACTIONf_plane_restr0.0051289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2826-2.30850.31231900.27063448X-RAY DIFFRACTION63
2.3085-2.33570.32372320.26074622X-RAY DIFFRACTION85
2.3357-2.36420.26322620.24884852X-RAY DIFFRACTION88
2.3642-2.39410.29892430.23875052X-RAY DIFFRACTION92
2.3941-2.42560.2482620.23295222X-RAY DIFFRACTION95
2.4256-2.45880.21272720.21245397X-RAY DIFFRACTION99
2.4588-2.49390.22942810.20245417X-RAY DIFFRACTION99
2.4939-2.53110.21742640.1815476X-RAY DIFFRACTION100
2.5311-2.57060.23422730.17165493X-RAY DIFFRACTION100
2.5706-2.61270.23672810.16575466X-RAY DIFFRACTION100
2.6127-2.65780.19033180.16495461X-RAY DIFFRACTION100
2.6578-2.70610.21733160.17075454X-RAY DIFFRACTION100
2.7061-2.75810.22932610.17585532X-RAY DIFFRACTION100
2.7581-2.81430.21292650.17595447X-RAY DIFFRACTION100
2.8143-2.87550.18492900.15715461X-RAY DIFFRACTION100
2.8755-2.94230.20332990.15635422X-RAY DIFFRACTION99
2.9423-3.01580.20682760.15455504X-RAY DIFFRACTION100
3.0158-3.09730.19362960.16255454X-RAY DIFFRACTION100
3.0973-3.18830.21222870.17055498X-RAY DIFFRACTION100
3.1883-3.29110.1842510.15945500X-RAY DIFFRACTION100
3.2911-3.40850.17342480.15925531X-RAY DIFFRACTION100
3.4085-3.54480.20623270.14925356X-RAY DIFFRACTION99
3.5448-3.70580.18353120.1445429X-RAY DIFFRACTION99
3.7058-3.90080.15583010.12835428X-RAY DIFFRACTION100
3.9008-4.14450.13512770.11265458X-RAY DIFFRACTION99
4.1445-4.46350.12573560.10335354X-RAY DIFFRACTION99
4.4635-4.91080.12542590.09985436X-RAY DIFFRACTION99
4.9108-5.61710.1582970.1085434X-RAY DIFFRACTION99
5.6171-7.06060.16953400.12945397X-RAY DIFFRACTION99
7.0606-29.34260.17972680.15865421X-RAY DIFFRACTION98
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)
10.5496-0.2050.15420.9115-0.33261.8589-0.0230.1333-0.0826-0.1144-0.00160.02010.1469-0.15870.03470.2605-0.00760.03610.53440.00190.384567.6969-5.51110.6344
20.49840.13380.13981.587-0.42311.2773-0.02860.1307-0.1489-0.16340.03330.0410.2931-0.3659-0.0060.332-0.1420.05320.54950.00230.421954.6363-28.154931.201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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