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- PDB-5col: RIBOSOMAL PROTEIN L11 FROM METHANOCOCCUS JANNASCHII -

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Basic information

Entry
Database: PDB / ID: 5col
TitleRIBOSOMAL PROTEIN L11 FROM METHANOCOCCUS JANNASCHII
Components50S ribosomal protein L11
KeywordsTRANSLATION / Archaeal Proteins / Methanococcus / Protein Structure / RNA / Ribosomal Proteins / Ribosomes
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 ...Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsGabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L11 FROM METHANOCOCCUS JANNASCHII
Authors: Gabdulkhakov, A.G.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L11
B: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5116
Polymers35,0272
Non-polymers4844
Water50428
1
A: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5492
Polymers17,5131
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9624
Polymers17,5131
Non-polymers4483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.150, 88.050, 142.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 50S ribosomal protein L11 /


Mass: 17513.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rpl11, MJ0373 / Plasmid: pET-11c/MjaL11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: P54030

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Non-polymers , 5 types, 32 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM Sodium Citrate, pH 5.0, 0.1 M MgCl2, 27% PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625, 0.97917
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 13, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976251
20.979171
ReflectionResolution: 2.2→50 Å / Num. obs: 22254 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.25 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.57

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→44.03 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.413 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25237 1038 5 %RANDOM
Rwork0.21513 ---
obs0.21703 19710 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.403 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-0 Å2
2---5.16 Å2-0 Å2
3---6.6 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 31 28 2379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192387
X-RAY DIFFRACTIONr_bond_other_d0.0010.022442
X-RAY DIFFRACTIONr_angle_refined_deg1.7412.0113217
X-RAY DIFFRACTIONr_angle_other_deg0.83235678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2645307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.03527.10883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.9515460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.558155
X-RAY DIFFRACTIONr_chiral_restr0.0890.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.676.3061231
X-RAY DIFFRACTIONr_mcbond_other4.6616.3041230
X-RAY DIFFRACTIONr_mcangle_it6.8299.4441534
X-RAY DIFFRACTIONr_mcangle_other6.8289.4461535
X-RAY DIFFRACTIONr_scbond_it5.8366.9981154
X-RAY DIFFRACTIONr_scbond_other5.8376.9971152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.84410.2151680
X-RAY DIFFRACTIONr_long_range_B_refined11.43651.0552702
X-RAY DIFFRACTIONr_long_range_B_other11.43451.0662703
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 77 -
Rwork0.371 1454 -
obs--99.03 %

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