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- PDB-2fk6: Crystal Structure of RNAse Z/tRNA(Thr) complex -

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Basic information

Entry
Database: PDB / ID: 2fk6
TitleCrystal Structure of RNAse Z/tRNA(Thr) complex
Components
  • RIBONUCLEASE Z
  • TRNA(THR)
KeywordsHYDROLASE/RNA / PROTEIN-tRNA COMPLEX / ZINC-DEPENDENT METAL HYDROLASE / tRNA MATURASE / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


tRNase Z / 3'-tRNA processing endoribonuclease activity / zinc ion binding / identical protein binding
Similarity search - Function
Ribonuclease Z/BN / Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Ribonuclease Z
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi de la Sierra-Gallay, I. / Mathy, N. / Pellegrini, O. / Condon, C.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA.
Authors: Li de la Sierra-Gallay, I. / Mathy, N. / Pellegrini, O. / Condon, C.
#1: Journal: Nature / Year: 2005
Title: Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z
Authors: Li de la Sierra-Gallay, I. / Pellegrini, O. / Condon, C.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: TRNA(THR)
A: RIBONUCLEASE Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4405
Polymers61,0882
Non-polymers3533
Water19811
1
R: TRNA(THR)
A: RIBONUCLEASE Z
hetero molecules

R: TRNA(THR)
A: RIBONUCLEASE Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,88110
Polymers122,1754
Non-polymers7056
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Unit cell
Length a, b, c (Å)173.540, 42.400, 110.430
Angle α, β, γ (deg.)90.00, 121.42, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -X,Y,-Z

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Components

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RNA chain / Protein , 2 types, 2 molecules RA

#1: RNA chain TRNA(THR)


Mass: 25522.186 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: B.subtilis tRNAThr(encoded by the trn1-Thr gene) was transcribed in vitro as a precursor with 6 nt 3'-extension from PCR fragment generated from plasmid pHMT1, using oligonucleotides HP560 and CC079
References: GenBank: 32468687
#2: Protein RIBONUCLEASE Z / E.C.3.1.26.11 / RNase Z / tRNase Z / tRNA 3 endonuclease


Mass: 35565.523 Da / Num. of mol.: 1 / Mutation: I46M, L228M, H65A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: W168 / Gene: RNZ / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (LAMBDADE3)-RIL / References: UniProt: P54548, tRNase Z

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Non-polymers , 4 types, 14 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG MME 2000, 0.1M Na-MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG MME 200011
2Na-MES11
3PEG MME 200012
4Na-MES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9762 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 6, 2005
RadiationMonochromator: 2 SILICON CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→47.12 Å / Num. all: 15664 / Num. obs: 15022 / % possible obs: 96.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 250 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.8 / % possible all: 87.6

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Processing

Software
NameClassification
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y44

1y44


Resolution: 2.9→47.12 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 882652.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 747 5 %RANDOM
Rwork0.25 ---
obs0.251 15022 95.9 %-
all-15664 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.4769 Å2 / ksol: 0.399279 e/Å3
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1--19.63 Å20 Å213.54 Å2
2--0.44 Å20 Å2
3---19.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 1125 19 11 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it4.422
X-RAY DIFFRACTIONc_scangle_it7.272.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 114 5 %
Rwork0.346 2160 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2ion.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3dna-rna_rep.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4water_rep.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5ligand_xplor_par.txt&_1_TOPOLOGY_INFILE_5

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