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- PDB-4reo: Mutant ribosomal protein l1 from thermus thermophilus with threon... -

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Basic information

Entry
Database: PDB / ID: 4reo
TitleMutant ribosomal protein l1 from thermus thermophilus with threonine 217 replaced by valine
Components50S ribosomal protein L1
KeywordsRNA BINDING PROTEIN / Rossmann Fold / RIBOSOMAL PROTEIN
Function / homology
Function and homology information


regulation of translation / large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L1/L10, rRNA-binding domain / Ribosomal protein L1/L10, domain II / 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, rRNA-binding domain / Ribosomal protein L1/L10, domain II / 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
GLYCINE / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGabdulkhakov, A.G. / Nevskaya, N.A. / Tishchenko, S.V. / 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
DepositionSep 23, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionMar 18, 2015ID: 3U42
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 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

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Assembly

Deposited unit
A: 50S ribosomal protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,71210
Polymers24,8661
Non-polymers8469
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.990, 60.450, 43.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

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Components

#1: Protein 50S ribosomal protein L1


Mass: 24865.727 Da / Num. of mol.: 1 / Mutation: T217V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rplA, rpl1 / Plasmid: pET11a-PL/TthL1T217V / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27150
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 15 MG/ML L1 50 MM GLYCINE, INITIALLY AT PH 10 5% (V/V) METHANE PENTANEDIOL 1.2 M AMMONIUM SULFATE EQUILIBRATED AGAINST 2.4 M AMMONIUM SULFATE 7% (V/V) METHANE PENTANEDIOL, VAPOR DIFFUSION, ...Details: 15 MG/ML L1 50 MM GLYCINE, INITIALLY AT PH 10 5% (V/V) METHANE PENTANEDIOL 1.2 M AMMONIUM SULFATE EQUILIBRATED AGAINST 2.4 M AMMONIUM SULFATE 7% (V/V) METHANE PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 16, 2011
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.35→20.67 Å / Num. all: 177960 / Num. obs: 44873 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.96 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.025 / Rsym value: 0.029 / Net I/σ(I): 25.16
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 3.95 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.53 / Num. unique all: 6241 / Rsym value: 0.447 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1AD2

1ad2


Resolution: 1.35→19.855 Å / SU ML: 0.14 / σ(F): 2 / Phase error: 18.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2242 5 %RANDOM
Rwork0.1672 ---
obs0.1694 44840 99.63 %-
all-45038 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→19.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 51 146 1877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061907
X-RAY DIFFRACTIONf_angle_d1.1162603
X-RAY DIFFRACTIONf_dihedral_angle_d12.53753
X-RAY DIFFRACTIONf_chiral_restr0.077293
X-RAY DIFFRACTIONf_plane_restr0.004342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.37940.28391390.2362639X-RAY DIFFRACTION100
1.3794-1.41140.26461380.22542629X-RAY DIFFRACTION100
1.4114-1.44670.27011380.21892614X-RAY DIFFRACTION100
1.4467-1.48580.25131380.20372631X-RAY DIFFRACTION100
1.4858-1.52950.24791380.18592623X-RAY DIFFRACTION100
1.5295-1.57890.21611390.16932639X-RAY DIFFRACTION100
1.5789-1.63530.22721400.16422663X-RAY DIFFRACTION100
1.6353-1.70070.20741400.16682650X-RAY DIFFRACTION100
1.7007-1.77810.21181400.15912656X-RAY DIFFRACTION100
1.7781-1.87180.20891380.16282640X-RAY DIFFRACTION100
1.8718-1.98890.1631410.15032663X-RAY DIFFRACTION100
1.9889-2.14230.1631400.14792671X-RAY DIFFRACTION100
2.1423-2.35760.18421410.15032669X-RAY DIFFRACTION100
2.3576-2.6980.18861420.16582696X-RAY DIFFRACTION100
2.698-3.39650.19871430.16342730X-RAY DIFFRACTION99
3.3965-19.85720.2331470.16962785X-RAY DIFFRACTION97

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