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- PDB-3u56: Crystal structure of mutant ribosomal protein T217V TthL1 in comp... -

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Basic information

Entry
Database: PDB / ID: 3u56
TitleCrystal structure of mutant ribosomal protein T217V TthL1 in complex with 80nt 23S RNA from Thermus thermophilus
Components
  • 50S ribosomal protein L1
  • RNA (80-MER)
KeywordsRNA/RNA BINDING PROTEIN / Rossmann Fold / RIBOSOMAL PROTEIN / rRNA / RIBOSOME / L1 protuberance in the ribosome / RNA-RNA BINDING PROTEIN 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
MALONATE ION / RNA / RNA (> 10) / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGabdulkhakov, A.G. / Nevskaya, N.A. / NIkonov, S.V.
CitationJournal: To be Published
Title: Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s rna from thermus thermophilus
Authors: Tishchenko, S.V. / Nikonova, E.Y. / Kostareva, O.S. / Gabdulkhakov, A.G. / Sarskikh, A.V. / Piendl, W. / Nikonov, S.V. / Garber, M.B. / Nevskaya, N.A.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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 / _struct_conn.pdbx_dist_value / _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.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_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: RNA (80-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,21014
Polymers50,8402
Non-polymers36912
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-128 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.690, 75.410, 85.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 50S ribosomal protein L1


Mass: 24865.727 Da / Num. of mol.: 1 / Mutation: V218R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rplA, rpl1 / Plasmid: pET11a-PL/TthL1 T217V / Production host: Escherichia coli (E. coli) / Strain (production host): BL11(DE3) / References: UniProt: P27150
#2: RNA chain RNA (80-MER)


Mass: 25974.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fragment of 23S rRNA / Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pUC18/rRNATth / Production host: Escherichia coli (E. coli) / Strain (production host): BL11(DE3)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 295 K / pH: 5.6
Details: 50mM NaCl, 2.5M Ammonium sulfate, 50mM MES, 10mM Magnesium acetate , pH 5.6, 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
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 18, 2011
RadiationMonochromator: MONTEL 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→28.3 Å / Num. obs: 28142 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.126 / Net I/σ(I): 12.57
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.01 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.38 / Rsym value: 0.341 / % possible all: 90

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AD2, 1MZP

1ad2

1mzp


Resolution: 2.1→28.3 Å / SU ML: 0.28 / σ(F): 2.05 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1407 5 %
Rwork0.191 --
obs0.194 28129 99.1 %
all-28129 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.72 Å2 / ksol: 0.43 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9157 Å20 Å2-0 Å2
2--4.4921 Å2-0 Å2
3----2.5764 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 1723 18 147 3630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063722
X-RAY DIFFRACTIONf_angle_d0.9355432
X-RAY DIFFRACTIONf_dihedral_angle_d15.521646
X-RAY DIFFRACTIONf_chiral_restr0.059670
X-RAY DIFFRACTIONf_plane_restr0.005399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1047-2.17990.29761300.27632461X-RAY DIFFRACTION94
2.1799-2.26710.30241400.24472664X-RAY DIFFRACTION100
2.2671-2.37030.30091390.24512642X-RAY DIFFRACTION100
2.3703-2.49520.30411400.24182647X-RAY DIFFRACTION100
2.4952-2.65140.34011410.24262678X-RAY DIFFRACTION100
2.6514-2.85590.27521400.22272677X-RAY DIFFRACTION100
2.8559-3.1430.251420.19572685X-RAY DIFFRACTION100
3.143-3.5970.221420.16892709X-RAY DIFFRACTION100
3.597-4.52890.16491440.13652730X-RAY DIFFRACTION100
4.5289-28.33510.18821490.15762829X-RAY DIFFRACTION99

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