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

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Basic information

Entry
Database: PDB / ID: 4tzw
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 replacing Mg2+ with Sr2+ post crystallization
Components
  • Ribosome-associated protein L7Ae-like
  • T-box Stem I
  • engineered tRNA
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 L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
STRONTIUM ION / RNA / RNA (> 10) / RNA (> 100) / RNA-binding protein YbxF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Oceanobacillus iheyensis HTE831 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.671 Å
AuthorsZhang, J. / Ferre-D'Amare, A.R.
Citation
Journal: Structure / Year: 2014
Title: Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.
Authors: Zhang, J. / Ferre-D'Amare, A.R.
#1: Journal: Nature / Year: 2013
Title: Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA.
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
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_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome-associated protein L7Ae-like
B: engineered tRNA
C: T-box Stem I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,01339
Polymers65,8593
Non-polymers3,15436
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint-1015 kcal/mol
Surface area31920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.316, 75.316, 268.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-101-

SR

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Components

#1: Protein Ribosome-associated protein L7Ae-like


Mass: 8492.660 Da / Num. of mol.: 1
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 tRNA


Mass: 24258.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#3: RNA chain T-box Stem I


Mass: 33107.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis HTE831 (bacteria)
#4: Chemical...
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Sr
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.56 % / Description: rectangular or rhombic plates
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: Jul 31, 2013
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: 4.67→45.79 Å / Num. obs: 4428 / % possible obs: 98.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.2
Reflection shellResolution: 4.67→4.84 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.9 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LCK

4lck


Resolution: 4.671→45.786 Å / SU ML: 0.78 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3312 766 10.03 %Random
Rwork0.2641 ---
obs0.2711 7638 97.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.671→45.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms524 3789 36 0 4349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094769
X-RAY DIFFRACTIONf_angle_d1.6817334
X-RAY DIFFRACTIONf_dihedral_angle_d17.7872286
X-RAY DIFFRACTIONf_chiral_restr0.069983
X-RAY DIFFRACTIONf_plane_restr0.007265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.671-5.03110.40411550.33931374X-RAY DIFFRACTION99
5.0311-5.53670.34681530.26351382X-RAY DIFFRACTION99
5.5367-6.3360.37071520.23771392X-RAY DIFFRACTION98
6.336-7.97590.38961510.3011369X-RAY DIFFRACTION97
7.9759-45.78860.29291550.24851355X-RAY DIFFRACTION96

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