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- PDB-1u63: THE STRUCTURE OF A RIBOSOMAL PROTEIN L1-mRNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1u63
TitleTHE STRUCTURE OF A RIBOSOMAL PROTEIN L1-mRNA COMPLEX
Components
  • 49 NT FRAGMENT OF MRNA FOR L1
  • 50S ribosomal protein L1PRibosome
KeywordsTRANSCRIPTION/RNA / RIBOSOME / RIBOSOMAL PROTEIN / MRNA-PROTEIN COMPLEX / TRANSCRIPTION-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 / Ribosomal protein L1, archaea / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / 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 / Ribosomal protein L1, archaea / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / 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
RNA / RNA (> 10) / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.4 Å
AuthorsNevskaya, N. / Tishchenko, S. / Gabdoulkhakov, A. / Nikonova, E. / Nikonov, O. / Nikulin, A. / Garber, M. / Nikonov, S. / Piendl, W.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA.
Authors: Nevskaya, N. / Tishchenko, S. / Gabdoulkhakov, A. / Nikonova, E. / Nikonov, O. / Nikulin, A. / Platonova, O. / Garber, M. / Nikonov, S. / Piendl, W.
History
DepositionJul 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2016Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 49 NT FRAGMENT OF MRNA FOR L1
D: 49 NT FRAGMENT OF MRNA FOR L1
A: 50S ribosomal protein L1P
C: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)81,9834
Polymers81,9834
Non-polymers00
Water0
1
B: 49 NT FRAGMENT OF MRNA FOR L1
A: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)40,9912
Polymers40,9912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 49 NT FRAGMENT OF MRNA FOR L1
C: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)40,9912
Polymers40,9912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.290, 68.900, 115.870
Angle α, β, γ (deg.)90.00, 122.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain 49 NT FRAGMENT OF MRNA FOR L1


Mass: 15867.548 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: SYNTHESIS OF THE RNA FRAGMENT FROM THE PLASMID pUC18, SEQUENCE FROM CELL-FREE(IN VITRO) SYSTEM WITHOUT LIVING ORGANISM
#2: Protein 50S ribosomal protein L1P / Ribosome


Mass: 25123.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rpl1p / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P54050

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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: 4.61 Å3/Da / Density % sol: 73.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 10000, MPD, KCL, NACl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 1000011
2MPD11
3KCL11
4NAClSodium chloride11
5H2O11
6PEG 1000012
7MPD12
8KCL12
9NAClSodium chloride12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.97895, 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 20, 2003 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978951
21.051
ReflectionResolution: 3.4→20 Å / Num. obs: 17645 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.901 % / Biso Wilson estimate: 75 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.062 / Net I/σ(I): 9.68
Reflection shellResolution: 3.4→3.61 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.79 / Num. unique all: 2718 / Rsym value: 0.318 / % possible all: 83.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 3.4→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 3657274.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.302 941 5.6 %RANDOM
Rwork0.276 ---
obs0.276 16760 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.7233 Å2 / ksol: 0.185876 e/Å3
Displacement parametersBiso mean: 84.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.98 Å0.88 Å
Refinement stepCycle: LAST / Resolution: 3.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 2110 0 0 5510
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d4.07
X-RAY DIFFRACTIONc_mcbond_it16.091.5
X-RAY DIFFRACTIONc_mcangle_it25.322
X-RAY DIFFRACTIONc_scbond_it16.072
X-RAY DIFFRACTIONc_scangle_it20.842.5
LS refinement shellResolution: 3.4→3.59 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.448 133 4.8 %
Rwork0.394 2646 -
obs--92.4 %
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

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