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- PDB-3qoy: Crystal structure of ribosomal protein L1 from Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 3qoy
TitleCrystal structure of ribosomal protein L1 from Aquifex aeolicus
Components50S ribosomal protein L1
KeywordsRIBOSOMAL PROTEIN / Beta-Alpha-Beta / structural constituent of ribosome / rRNA binding / regulation of translation / translation / Ribosomal RNA / mRNA / Ribosomal Proteins
Function / homology
Function and homology information


maturation of LSU-rRNA / regulation of translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / RNA binding
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
ACETIC ACID / 50S ribosomal protein L1
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, S.V. / Nikonova, E.U. / Shkliaeva, A.A. / Garber, M.B. / Nikonov, S.V. / Nevskaya, N.A.
CitationJournal: Crystallography Reports / Year: 2011
Title: Crystal Structure of Ribosomal Protein L1 from the Bacterium Aquifex Aeolicus
Authors: Nikonova, E.Yu. / Tishchenko, S.V. / Gabdulkhakov, A.G. / Shklyaeva, A.A. / Garber, M.B. / Nikonov, S.V. / Nevskaya, N.A.
History
DepositionFeb 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)27,3285
Polymers26,9541
Non-polymers3744
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.490, 37.520, 58.970
Angle α, β, γ (deg.)90.00, 110.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-315-

HOH

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Components

#1: Protein 50S ribosomal protein L1 /


Mass: 26953.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1935, rplA / Plasmid: pET11a-PL-AaeL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O67759
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25 % PEG4000, 100mM acetate buffer, 200mM ammonium sulphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54189 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 19, 2011
RadiationMonochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54189 Å / Relative weight: 1
ReflectionResolution: 2.1→28.67 Å / Num. all: 13162 / Num. obs: 12221 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.39 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.098 / Net I/σ(I): 11.94
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.85 / Num. unique all: 1693 / Rsym value: 0.289 / % possible all: 83.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AD2

1ad2


Resolution: 2.1→19.653 Å / SU ML: 0.25 / σ(F): 2.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 611 5 %RANDOM
Rwork0.1937 ---
all0.1971 13162 --
obs0.1967 12219 93.16 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.552 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1461 Å2-0 Å20.097 Å2
2---3.4497 Å20 Å2
3---1.3035 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 22 77 1985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081955
X-RAY DIFFRACTIONf_angle_d1.1462634
X-RAY DIFFRACTIONf_dihedral_angle_d16.894777
X-RAY DIFFRACTIONf_chiral_restr0.073297
X-RAY DIFFRACTIONf_plane_restr0.004337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1-2.31110.29411420.21892700270088
2.3111-2.64480.28261510.20682879287993
2.6448-3.32960.2641560.20132962296295
3.3296-19.65370.21221620.17253067306796

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