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- PDB-3t3n: Molecular basis for the recognition and cleavage of RNA (UUCCGU) ... -

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Basic information

Entry
Database: PDB / ID: 3t3n
TitleMolecular basis for the recognition and cleavage of RNA (UUCCGU) by the bifunctional 5'-3' exo/endoribonuclease RNase J
Components
  • Metal dependent hydrolase
  • O2'methyl-RNA
KeywordsHYDROLASE/RNA / PROTEIN-RNA COMPLEX / Metallo-beta-lactamase / RNase J / Endoribonuclease / 5'-3' Exoribonuclease / Metal dependent hydrolase / RNA / hydrolase / HYDROLASE-RNA complex
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 / identical protein binding / cytoplasm
Similarity search - Function
Ubiquitin-like (UB roll) - #580 / 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 / Beta-lactamase superfamily domain ...Ubiquitin-like (UB roll) - #580 / 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 / Beta-lactamase superfamily domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Sugar transport proteins signature 1. / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / 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
RNA / Ribonuclease J
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsDorleans, A. / Li de la Sierra-Gallay, I. / Piton, J. / Zig, L. / Gilet, L. / Putzer, H. / Condon, C.
CitationJournal: Structure / Year: 2011
Title: Molecular Basis for the Recognition and Cleavage of RNA by the Bifunctional 5'-3' Exo/Endoribonuclease RNase J.
Authors: Dorleans, A. / Li de la Sierra-Gallay, I. / Piton, J. / Zig, L. / Gilet, L. / Putzer, H. / Condon, C.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Derived calculations
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Metal dependent hydrolase
B: O2'methyl-RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5913
Polymers64,5262
Non-polymers651
Water23413
1
A: Metal dependent hydrolase
B: O2'methyl-RNA
hetero molecules

A: Metal dependent hydrolase
B: O2'methyl-RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1826
Polymers129,0514
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area28000 Å2
ΔGint-161 kcal/mol
Surface area85000 Å2
Unit cell
Length a, b, c (Å)101.950, 116.780, 231.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Metal dependent hydrolase


Mass: 62612.379 Da / Num. of mol.: 1 / Mutation: H77A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / Gene: ttc0775, TT_C0775 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q72JJ7, Hydrolases
#2: RNA chain O2'methyl-RNA


Mass: 1913.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 16-nt 2'-O-methylated RNA
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2-4% PEG 4K, 0.02M ammonium sulfate, 0.1M Na-MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2010
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationMonochromator: cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.09→55 Å / Num. all: 12981 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 72.03 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.67
Reflection shellResolution: 3.1→3.25 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.93 / % possible all: 85.1

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Processing

Software
NameVersionClassification
XDSPackagedata scaling
PHASERphasing
BUSTER2.8.0refinement
XDSPackagedata reduction
XDSCONVdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BK1

3bk1


Resolution: 3.09→54.41 Å / Cor.coef. Fo:Fc: 0.9262 / Cor.coef. Fo:Fc free: 0.8728 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 1004 8.16 %RANDOM
Rwork0.2019 ---
obs0.2066 12301 --
all-13183 --
Displacement parametersBiso mean: 77.21 Å2
Baniso -1Baniso -2Baniso -3
1-12.1489 Å20 Å20 Å2
2---1.4673 Å20 Å2
3----10.6816 Å2
Refine analyzeLuzzati coordinate error obs: 0.585 Å
Refinement stepCycle: LAST / Resolution: 3.09→54.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 130 1 13 4455
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084550HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.096184HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1612SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes111HARMONIC2
X-RAY DIFFRACTIONt_gen_planes653HARMONIC5
X-RAY DIFFRACTIONt_it4550HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.47
X-RAY DIFFRACTIONt_other_torsion20.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion590SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4849SEMIHARMONIC4
LS refinement shellResolution: 3.09→3.38 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2922 232 8.16 %
Rwork0.2483 2611 -
all0.2519 2843 -

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