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- PDB-4lq4: crystal structure of mutant ribosomal protein L1 from Methanococc... -

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Basic information

Entry
Database: PDB / ID: 4lq4
Titlecrystal structure of mutant ribosomal protein L1 from Methanococcus jannaschii with deletion of 8 residues from C-terminus
Components50S ribosomal protein L1
KeywordsRIBOSOMAL PROTEIN / Beta-Alpha-Beta / structural constituent of ribosome / rRNA binding / regulation of translation / translation / Ribosomal RNA / mRNA
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 signature. / Ribosomal protein L1 / 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 signature. / Ribosomal protein L1 / 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
ISOPROPYL ALCOHOL / L(+)-TARTARIC ACID / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, S.V. / Shkliaeva, A.A. / Garber, M.B. / Nikonov, S.V. / Sarskikh, A.V.
CitationJournal: Crystallography Reports / Year: 2014
Title: Crystal structure of a mutant of archaeal ribosomal protein L1 from Methanococcus jannaschii
Authors: Sarskikh, A.V. / Gabdulkhakov, A.G. / Kostareva, O.S. / Shkliaeva, A.A. / Tishchenko, S.V.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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)24,1846
Polymers23,8671
Non-polymers3175
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.868, 105.255, 38.526
Angle α, β, γ (deg.)90.00, 104.01, 90.00
Int Tables number4
Space group name H-MP1211
Detailspart of ribosome

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Components

#1: Protein 50S ribosomal protein L1 /


Mass: 23867.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0510, rpl1, rplA / Plasmid: pET11a-PL-MjaL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54050
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 10% isopropanol, 0.1 M Hepes-NaOH, 0.5 mkl 0.8 KNa-tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54189 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 27, 2010
RadiationMonochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54189 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. all: 26394 / Num. obs: 26074 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.34 Å2
Reflection shellResolution: 1.75→1.85 Å / % possible all: 93.4

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1389)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I2A

1i2a


Resolution: 1.75→32.86 Å / SU ML: 0.2 / σ(F): 1.19 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 2365 5.07 %RANDOM
Rwork0.1644 ---
obs0.1673 26039 89.62 %-
all-26074 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→32.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 17 219 1910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061715
X-RAY DIFFRACTIONf_angle_d1.0512304
X-RAY DIFFRACTIONf_dihedral_angle_d12.661687
X-RAY DIFFRACTIONf_chiral_restr0.073265
X-RAY DIFFRACTIONf_plane_restr0.005295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78570.34111150.29211981X-RAY DIFFRACTION66
1.7857-1.82450.27971200.23212005X-RAY DIFFRACTION72
1.8245-1.8670.24941400.2022228X-RAY DIFFRACTION76
1.867-1.91370.2513920.19552282X-RAY DIFFRACTION78
1.9137-1.96540.23731060.18122424X-RAY DIFFRACTION83
1.9654-2.02320.2771420.1772489X-RAY DIFFRACTION86
2.0232-2.08850.20961170.15922560X-RAY DIFFRACTION88
2.0885-2.16320.21021100.15012684X-RAY DIFFRACTION91
2.1632-2.24970.20861650.142745X-RAY DIFFRACTION93
2.2497-2.35210.19461420.14972739X-RAY DIFFRACTION96
2.3521-2.47610.23741400.1582873X-RAY DIFFRACTION98
2.4761-2.63110.19871680.16892865X-RAY DIFFRACTION99
2.6311-2.83420.23311470.18882905X-RAY DIFFRACTION99
2.8342-3.11920.24131600.18652867X-RAY DIFFRACTION99
3.1192-3.57010.24571690.1692862X-RAY DIFFRACTION99
3.5701-4.49610.18241630.13912899X-RAY DIFFRACTION100
4.4961-32.86620.17951690.13262895X-RAY DIFFRACTION100

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