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- PDB-1mzp: Structure of the L1 protuberance in the ribosome -

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Basic information

Entry
Database: PDB / ID: 1mzp
TitleStructure of the L1 protuberance in the ribosome
Components
  • 50s ribosomal protein L1PRibosome
  • fragment of 23S rRNA
KeywordsRIBOSOME / ribosomal protein / RNA-protein complex
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, 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 speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsNikulin, A. / Eliseikina, I. / Tishchenko, S. / Nevskaya, N. / Davydova, N. / Platonova, O. / Piendl, W. / Selmer, M. / Liljas, A. / Zimmermann, R. ...Nikulin, A. / Eliseikina, I. / Tishchenko, S. / Nevskaya, N. / Davydova, N. / Platonova, O. / Piendl, W. / Selmer, M. / Liljas, A. / Zimmermann, R. / Garber, M. / Nikonov, S.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure of the L1 protuberance in the ribosome.
Authors: Nikulin, A. / Eliseikina, I. / Tishchenko, S. / Nevskaya, N. / Davydova, N. / Platonova, O. / Piendl, W. / Selmer, M. / Liljas, A. / Drygin, D. / Zimmermann, R. / Garber, M. / Nikonov, S.
History
DepositionOct 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: fragment of 23S rRNA
A: 50s ribosomal protein L1P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6005
Polymers42,5272
Non-polymers733
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.010, 156.010, 90.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: RNA chain fragment of 23S rRNA


Mass: 17836.684 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesis of the RNA fragment from the plasmid pDD55; sequence from cell-free(in vitro) system without living organism.
#2: Protein 50s ribosomal protein L1P / Ribosome


Mass: 24690.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Description: AUTHOR STATES TO AVOID THE POTENTIAL MISINCORPORATION OF LYSINE INSTEAD OF ARGININE, THE HOST STRAIN WAS COTRANSFORMED WITH PUBS520, A PLASMID CARRYING THE GENE FOR TRNA(ARG)AGA-AGG.
Plasmid: pSacL1.4 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P35024
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.78 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG400, Tris HCl, KCl, MgCl2, ph 8.5, VAPOR DIFFUSION, HANGING DROP at 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2Tris HCl11
3KCl11
4MgCl211
5PEG 40012
6KCl12
7MgCl212
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %(v/v)PEG4001drop
250 mM1droppH8.6
3100 mM1dropKCl
410 mM1dropMgCl2
54 %(v/v)glycerol1drop
63 mg/mlRNA1drop
74.8 mg/mlSacL11drop
827 %(v/v)PEG4001reservoir
950 mMTris-HCl1reservoirpH8.5
10100 mM1reservoirKCl
1110 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9762,0.9330
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2002
RadiationMonochromator: Double crystal focusing monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.9331
ReflectionResolution: 2.65→25 Å / Num. all: 22839 / Num. obs: 22839 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.65→2.7 Å / Rmerge(I) obs: 0.376 / % possible all: 97.2
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 35675 / Num. measured all: 277313
Reflection shell
*PLUS
% possible obs: 97.2 % / Mean I/σ(I) obs: 6

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1263310.5 / Data cutoff high rms absF: 1263310.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 952 5 %RANDOM
Rwork0.219 ---
all0.259 19127 --
obs0.219 19127 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.521 Å2 / ksol: 0.32442 e/Å3
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.16 Å25.66 Å20 Å2
2--6.16 Å20 Å2
3----12.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 1185 3 94 3002
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.39
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.421 94 5.1 %
Rwork0.338 1740 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.39

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