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- PDB-4tzz: Co-crystals of the Ternary Complex Containing a T-box Stem I RNA,... -

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Basic information

Entry
Database: PDB / ID: 4tzz
TitleCo-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate and increasing PEG3350 concentration from 20% to 45% post crystallization
Components
  • Ribosome-associated protein L7Ae-like
  • T-box Stem I RNA
  • engineered tRNAGly
KeywordsRIBOSOMAL PROTEIN/RNA / RNA / riboswitch / tRNA / T-box / RIBOSOMAL PROTEIN-RNA complex
Function / homology
Function and homology information


ribosome / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, putative / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA-binding protein YbxF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Oceanobacillus iheyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.64 Å
AuthorsZhang, J. / Ferre-D'Amare, A.R.
CitationJournal: Structure / Year: 2014
Title: Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.
Authors: Zhang, J. / Ferre-D'Amare, A.R.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_keywords.text
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosome-associated protein L7Ae-like
B: engineered tRNAGly
C: T-box Stem I RNA
D: Ribosome-associated protein L7Ae-like
E: engineered tRNAGly
F: T-box Stem I RNA
G: Ribosome-associated protein L7Ae-like
H: engineered tRNAGly
I: T-box Stem I RNA
J: Ribosome-associated protein L7Ae-like
K: engineered tRNAGly
L: T-box Stem I RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,14041
Polymers263,43512
Non-polymers70529
Water00
1
A: Ribosome-associated protein L7Ae-like
B: engineered tRNAGly
C: T-box Stem I RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0059
Polymers65,8593
Non-polymers1466
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ribosome-associated protein L7Ae-like
E: engineered tRNAGly
F: T-box Stem I RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,12614
Polymers65,8593
Non-polymers26711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Ribosome-associated protein L7Ae-like
H: engineered tRNAGly
I: T-box Stem I RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,10213
Polymers65,8593
Non-polymers24310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Ribosome-associated protein L7Ae-like
K: engineered tRNAGly
L: T-box Stem I RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9075
Polymers65,8593
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.641, 260.733, 70.698
Angle α, β, γ (deg.)90.00, 92.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribosome-associated protein L7Ae-like


Mass: 8492.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rplGB, ybaB, ybxF, BSU01090 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P46350
#2: RNA chain
engineered tRNAGly


Mass: 24258.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#3: RNA chain
T-box Stem I RNA


Mass: 33107.746 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Mg

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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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM Bis-Tris (HCl) pH 6.5, 300 mM Li2SO4, and 20% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 3, 2012
RadiationMonochromator: Kohzu HLD8-24 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.64→70.61 Å / Num. obs: 24059 / % possible obs: 84.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.1
Reflection shellResolution: 3.64→3.77 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2.9 / % possible all: 85.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LCK

4lck


Resolution: 3.64→70.61 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 1230 5.11 %Random
Rwork0.2171 ---
obs0.22 24051 84.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.64→70.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 15149 29 0 17274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219077
X-RAY DIFFRACTIONf_angle_d0.49329338
X-RAY DIFFRACTIONf_dihedral_angle_d16.7059142
X-RAY DIFFRACTIONf_chiral_restr0.0233930
X-RAY DIFFRACTIONf_plane_restr0.0021060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.64-3.78460.31351250.28312541X-RAY DIFFRACTION84
3.7846-3.95690.29061480.25592601X-RAY DIFFRACTION87
3.9569-4.16550.28541280.23712614X-RAY DIFFRACTION86
4.1655-4.42640.29381440.2352566X-RAY DIFFRACTION85
4.4264-4.76810.28441440.22572502X-RAY DIFFRACTION85
4.7681-5.24780.2511280.22862583X-RAY DIFFRACTION85
5.2478-6.00680.27971190.19662525X-RAY DIFFRACTION83
6.0068-7.56650.28441420.21182474X-RAY DIFFRACTION83
7.5665-70.6270.24391520.19832415X-RAY DIFFRACTION80

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