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- PDB-2oum: The first domain of L1 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 2oum
TitleThe first domain of L1 from Thermus thermophilus
Components50S ribosomal protein L1
KeywordsRIBOSOMAL PROTEIN / ribosomal protein L1 / Thermus thermophilus
Function / homology
Function and homology information


regulation of translation / large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
50S ribosomal protein L1; Chain A, Domain 1 / Arc Repressor Mutant, subunit A / 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 ...50S ribosomal protein L1; Chain A, Domain 1 / Arc Repressor Mutant, subunit A / 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 / Helix non-globular / Special
Similarity search - Domain/homology
Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKljashtorny, V. / Tishchenko, S. / Nevskaya, N. / Nikonov, S. / Davydova, N. / Garber, M.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Domain I of ribosomal protein L1 is sufficient for specific RNA binding.
Authors: Tishchenko, S. / Nikonova, E. / Kljashtorny, V. / Kostareva, O. / Nevskaya, N. / Piendl, W. / Davydova, N. / Streltsov, V. / Garber, M. / Nikonov, S.
History
DepositionFeb 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND RESIDUES 1-67 AND 159-228 ARE COVALENTLY LINKED TO EACH OTHER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L1


Theoretical massNumber of molelcules
Total (without water)15,1711
Polymers15,1711
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.700, 45.320, 37.890
Angle α, β, γ (deg.)90.00, 100.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 50S ribosomal protein L1 /


Mass: 15171.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: Pdom1TthL1.4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27150, UniProt: Q5SLP7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.86 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 30% v/v polyethylenglycol 4K, 100 mM Tris-HCl, 200 mM acetate Na, pH 8.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.55→15 Å / Num. all: 3594 / Num. obs: 3392 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.119 / Net I/σ(I): 8.8
Reflection shellResolution: 2.55→2.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.5 / Num. unique all: 202 / Rsym value: 0.351 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The first domain of L1 from Thermus thermophilus

Resolution: 2.55→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.297 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26973 154 4.4 %RANDOM
Rwork0.17737 ---
all0.18147 3356 --
obs0.18147 3356 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.255 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å2-0.07 Å2
2---0.46 Å20 Å2
3---2.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å
Refinement stepCycle: LAST / Resolution: 2.55→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 0 23 1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.321.9671389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4125130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.42623.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.32115175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.82159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02780
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.8375
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.8685
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.855
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.834
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.810
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.1954659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it11.28951050
X-RAY DIFFRACTIONr_scbond_it9.5434376
X-RAY DIFFRACTIONr_scangle_it12.3185338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 17 -
Rwork0.227 241 -
obs-241 100 %

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