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- PDB-4qg3: Crystal structure of mutant ribosomal protein G219V TthL1 in comp... -

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Basic information

Entry
Database: PDB / ID: 4qg3
TitleCrystal structure of mutant ribosomal protein G219V 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 / rRNA BINDING / RIBOSOME / RIBOSOMAL PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of translation / cytosolic large ribosomal subunit / 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
BETA-MERCAPTOETHANOL / ISOPROPYL ALCOHOL / UREA / RNA / RNA (> 10) / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 20, 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 / 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 / _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: 50S ribosomal protein L1
B: fragment of 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,08720
Polymers50,7532
Non-polymers1,33418
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-73 kcal/mol
Surface area22580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.773, 76.489, 86.254
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 , 2 types, 2 molecules AB

#1: Protein 50S ribosomal protein L1


Mass: 24778.582 Da / Num. of mol.: 1 / Mutation: G219V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rplA, rpl1 / Plasmid: pET11a-PL/TthL1 G219V / 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 / Fragment: 80 nt fragment of 23S rRNA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pUC18/rRNATth / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 279 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 47.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8 M Ammonium sulfate, 0.05 M Bis-Tris,pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Mar 1, 2013
RadiationMonochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 33273 / Num. obs: 33152 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.1 Å / % possible all: 99.3

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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: 2→22.981 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1506 4.77 %RANDOM
Rwork0.1998 ---
all0.205 33273 --
obs0.201 31564 95.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→22.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 1723 77 261 3806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093783
X-RAY DIFFRACTIONf_angle_d1.2475501
X-RAY DIFFRACTIONf_dihedral_angle_d13.8421652
X-RAY DIFFRACTIONf_chiral_restr0.052671
X-RAY DIFFRACTIONf_plane_restr0.007400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06450.32681330.28692637X-RAY DIFFRACTION92
2.0645-2.13830.3211480.26322581X-RAY DIFFRACTION93
2.1383-2.22380.27021420.2382628X-RAY DIFFRACTION93
2.2238-2.32490.26451240.21672606X-RAY DIFFRACTION92
2.3249-2.44740.2341260.20672619X-RAY DIFFRACTION92
2.4474-2.60050.23651280.21012633X-RAY DIFFRACTION92
2.6005-2.8010.29751120.25162776X-RAY DIFFRACTION96
2.801-3.08230.24141840.23542784X-RAY DIFFRACTION98
3.0823-3.52690.19781280.18222884X-RAY DIFFRACTION99
3.5269-4.43830.14481310.1452915X-RAY DIFFRACTION99
4.4383-22.9830.19731500.16252995X-RAY DIFFRACTION98

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