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- PDB-2hw8: Structure of ribosomal protein L1-mRNA complex at 2.1 resolution. -

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Basic information

Entry
Database: PDB / ID: 2hw8
TitleStructure of ribosomal protein L1-mRNA complex at 2.1 resolution.
Components
  • 36-MER
  • 50S ribosomal protein L1
KeywordsSTRUCTURAL PROTEIN/RNA / ribosomal protein L1 / mRNA / RNA-protein complex / STRUCTURAL 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 / Ribosomal protein L1 signature. / 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 / Ribosomal protein L1 signature. / 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
1,4-BUTANEDIOL / : / RNA / RNA (> 10) / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTishchenko, S. / Nikonova, E. / Nikulin, A. / Nevskaya, N. / Volchkov, S. / Piendl, W. / Garber, M. / Nikonov, S.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: Structure of the ribosomal protein L1-mRNA complex at 2.1 A resolution: common features of crystal packing of L1-RNA complexes.
Authors: Tishchenko, S. / Nikonova, E. / Nikulin, A. / Nevskaya, N. / Volchkov, S. / Piendl, W. / Garber, M. / Nikonov, S.
History
DepositionAug 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_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.pdbx_leaving_atom_flag / _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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 36-MER
A: 50S ribosomal protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6845
Polymers36,5302
Non-polymers1543
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.870, 67.870, 340.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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RNA chain / Protein , 2 types, 2 molecules BA

#1: RNA chain 36-MER


Mass: 11634.986 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA WAS PREPARED FROM THE PLASMID IN CELL-FREE (IN VITRO) SYSTEM WITHOUT LIVING ORGANISM
#2: Protein 50S ribosomal protein L1 /


Mass: 24895.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: VK1 / Gene: rpl1 / Plasmid: pACA-L1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27150

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Non-polymers , 4 types, 166 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG1000, sodium cacodylate,0.5% glycerol, 0.2 mM HgCl2 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG100011
2sodium cacodylate11
3glycerol11
4HgCl211
5H2O11
6PEG100012
7sodium cacodylate12
8glycerol12
9HgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 22, 2004
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 28370 / Num. obs: 28370 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.9
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4.3 / Num. unique all: 4317 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZHO

1zho


Resolution: 2.1→25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3103802.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1382 4.9 %RANDOM
Rwork0.212 ---
all0.237 28370 --
obs0.212 28370 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.7043 Å2 / ksol: 0.322747 e/Å3
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.76 Å2-0.13 Å20 Å2
2---5.76 Å20 Å2
3---11.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-25 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 774 8 163 2687
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it31.5
X-RAY DIFFRACTIONc_mcangle_it3.932
X-RAY DIFFRACTIONc_scbond_it4.422
X-RAY DIFFRACTIONc_scangle_it5.212.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 231 5.1 %
Rwork0.31 4342 -
obs-4342 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5bu1.parambu1.top

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