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- PDB-4qvi: Crystal structure of mutant ribosomal protein M218L TthL1 in comp... -

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Basic information

Entry
Database: PDB / ID: 4qvi
TitleCrystal structure of mutant ribosomal protein M218L TthL1 in complex with 80nt 23S RNA from Thermus thermophilus
Components
  • 50S ribosomal protein L1
  • fragment of 23S rRNA
KeywordsRIBOSOMAL PROTEIN/RNA / Rossmann Fold / RIBOSOMAL PROTEIN / rRNA / RIBOSOME / L1 protuberance / RIBOSOMAL PROTEIN-RNA complex
Function / homology
Function and homology information


large ribosomal subunit / regulation of translation / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L1/L10, domain II / Ribosomal protein L1/L10, rRNA-binding domain / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein ...Ribosomal protein L1/L10, domain II / Ribosomal protein L1/L10, rRNA-binding domain / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / ACETATE ION / RNA / RNA (> 10) / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGabdulkhakov, A.G. / Nevskaya, N.A. / NIkonov, S.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions.
Authors: Tishchenko, S. / Kostareva, O. / Gabdulkhakov, A. / Mikhaylina, A. / Nikonova, E. / Nevskaya, N. / Sarskikh, A. / Piendl, W. / Garber, M. / Nikonov, S.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L1
B: fragment of 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,98212
Polymers50,8242
Non-polymers1,15810
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-83 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.136, 75.845, 86.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain / Sugars , 3 types, 3 molecules AB

#1: Protein 50S ribosomal protein L1


Mass: 24849.662 Da / Num. of mol.: 1 / Mutation: M218L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rplA, rpl1 / Plasmid: pET11a-PL/TthL1 M218L / Production host: Escherichia coli (E. coli) / Strain (production host): BL11(DE3) / References: UniProt: P27150
#2: RNA chain fragment of 23S rRNA


Mass: 25974.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pUC18/rRNATth / Production host: Escherichia coli (E. coli) / Strain (production host): BL11(DE3)
#3: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 346 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.5 M ammonium sulfate, 0.05M MES , 0.01M Magnesium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 18, 2014
RadiationMonochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→27.2 Å / Num. all: 38690 / Num. obs: 38405 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 98

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U4M

3u4m


Resolution: 1.9→23.465 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1909 5.09 %RANDOM
Rwork0.1939 ---
all0.1955 38405 --
obs0.1951 37533 97.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→23.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 1723 71 337 3881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063790
X-RAY DIFFRACTIONf_angle_d1.0275527
X-RAY DIFFRACTIONf_dihedral_angle_d13.871669
X-RAY DIFFRACTIONf_chiral_restr0.042679
X-RAY DIFFRACTIONf_plane_restr0.006404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.29311300.2792416X-RAY DIFFRACTION93
1.9475-2.00010.32731340.27012369X-RAY DIFFRACTION93
2.0001-2.0590.28651360.25622411X-RAY DIFFRACTION93
2.059-2.12540.26891170.24232439X-RAY DIFFRACTION95
2.1254-2.20130.28771430.2422496X-RAY DIFFRACTION96
2.2013-2.28930.24791250.23782523X-RAY DIFFRACTION97
2.2893-2.39340.25931270.22672543X-RAY DIFFRACTION97
2.3934-2.51950.25081330.23012557X-RAY DIFFRACTION98
2.5195-2.67710.27221290.23582575X-RAY DIFFRACTION99
2.6771-2.88350.27441660.23192565X-RAY DIFFRACTION99
2.8835-3.1730.22471220.20222655X-RAY DIFFRACTION100
3.173-3.63070.18531540.15562626X-RAY DIFFRACTION100
3.6307-4.56880.13681410.13112665X-RAY DIFFRACTION100
4.5688-23.46640.15711520.14612784X-RAY DIFFRACTION100

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